"convert colors" causes jpeg compression?

I recently had to re-install Acrobat, and since doing so whenever I run my preflight profile which is set to convert spot colors to cmyk, it's also apparently increasing the jpeg compression at the same time. Everything seems to be gaining bad jpeg artifacts after the color conversion (even when the colors being converted have nothing to do with the images).
It may be unrelated, but it also seems to be creating all sorts of ICC profile non-cmyk colors in the process. I.e., before "convert to cmyk for digital printing" I run a preflight that simply checks for non-cmyk colors. This profile warns me that there is a Pantone color in the ad. I check the separation preview and find only one or two things with Pantone colors. I then run the convert fix. The Pantone colors go away, but now there are sometimes dozens of items that are showing up as ICC profile colors, and this seems unfixable. I can't create a profile to convert them.
What's going on? Are there settings somewhere that can select the degree of (or lack of) jpeg compression? Why is it compressing the file at all? I have no such setting selected in the preflight profile. I tried creating a profile that does absolutely nothing at all but convert to cmyk, and it's still causing these problems.
This is using Acrobat 8. It's the same version, same disks, we used before, but these problems are new. I may have a setting wrong somewhere.

You are not making sense, and your methodology is fundamentally flawed.
Hitting Command+S without editing the file is NOT "saving".  It's not doing anything at all.  The program just idles.
You can verify this by observing that the file's modification date does not change.
Even your limited but flawed methodology will show the degradation if you change even a single pixel before hitting Command+S.  Then you will be degrading the image.  Just make a one-pixel change, for instance with the pencil tool, then save.  That is the same as doing a Save As.
Note that in your original query you were indeed changing a file by converting it to a different color space.  THAT is a change.
Independently from the above, your methodology of comparing two layers blended in Difference mode has the inherent limitation of the monitor's performance in displaying the shadows.  Your monitor, no matter how high-end, will NOT show you a difference between a 0,0,0 pixel (R,G,B,) and 0,0,1 or 1,0,0 or 1,0,1 for instance.  SAme goes for 1,0,2 etc., until you reach the lower threshold of your particular monitor.
There are two preferred methods of comparing two layers to see if they're identical.
Comparing allegedly identical images in Photoshop
The first one, championed by the late, lamented author and guru Bruce Fraser, is as follows [direct quote by copy and paste]:
A better way of comparing images with identical pixel dimensions is to use [Image menu >] Apply Image… > Subtract with an Offset of 128.
Difference only shows pixels that are lighter in the source than in the target (or maybe it's the other way around—I forget) where Subtract with Offset 128 shows differences in both directions.
Pixels that are identical in both images come in as RGB 128 gray, those that are different come in at a value that exactly reflects how different they are.
It also makes it much easier to spot subtle differences…
=== ===
The second one was suggested by someone in the Color Managament and Photoshop Windows forums, which follows:
(NOTE: only the methodology is of interest and pertinent, not the questionable context in which it has brought up and used.)
* 1) Open the two images to be compared in Photoshop
* 2) Move one image as a layer over the other one
* 3) select "Difference" as blending mode in the layers palette
* 4) now the whole image should appear seemingly black on the monitor
[So far this is the traditional, "time honored" method.]
* 5) select the magic wand tool with these settings: Tolerance: 0/ Anti-alias: no/ Contiguous: no/ Sample All Layers: yes
* 6) click somewhere into the formerly gray area
[This refers to an image of a Color-Checker type of card that had wide gray border around it. The test, therefore, requires a pure gray image in the image, something highly unlikely to change, in order for the magic wand to select all pure-black images (255,255,255). Such a border can easily be created around an image by increasing the canvas size and filling the newly created space with pure gray (128,128,128). ]
    Explanation: you just selected all completely black pixels (0,0,0) i.e. all pixels that are identical in both layers.
* 7) you should see "marching ants" forming rectangular patterns
* 8_) invert the selection (Shift Command I)
   Explanation: the selection now covers all the other pixels, i.e. all pixels which are different between both layers.
* 9) create a new empty layer and select it in the layers palette
* 10) set the foreground color to white
* 11) fill the selection with white (Alt+backspace on Windows, accordingly on Mac)
* 12) set the blending modes of all layers back to normal
    Explanation: you now see all identical pixels in their respective color and all different pixels in white.
This method is a lot more sensitive than the traditional one which stops at step #4 above.
Finally:
jfraze wrote:
Wow, the level of hostility is amazing on these adobe forums…
Only because people like you come in here itching for a fight, rather than to seek help.  It's just the way you choose to react—and to intereact with others.
Wo Tai Lao Le
我太老了

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    I haven't found any documentation of the meaning of the 0 - 100% JPEG compression value in LR's (v1 or v2) Export File window. And the default value of 100% is overkill and results in huge files. At least I'm familiar with the Photoshop's 0-12 JPEG quality scale with associated quality names: Low, Medium, High, and Maximum.
    Via trial and error, I have found that LR has the same 13 quality levels as Photoshop and gives the same results, they are just mapped on a 0 - 100% scale. This also means that changing a few percent may not make any change at all, since a quality change only happens about every 7 percent.
    For those who might find it useful, here is a table of the mappings:
    The first column is the Photoshop compression number and name; the second column in the range of Lightroom percentages that will give the same results.
    0-Low 0-7%
    1-Low 8-15%
    2-Low 16-23%
    3-Low 24-30%
    4-Low 31-38%
    5-Med 39-46%
    6-Med 47-53%
    7-Med 54-61%
    8-High 62-69%
    9-High 70-76%
    10-Max 77-84%
    11-Max 85-91%
    12-Max 92-100%

    I looked at this again using PS's 'Baseline Standard' JPEG format option instead of 'Baseline Optimized. LR does not provide the format options Standard, Optimized, and Progressive, but appears to use 'Baseline Standard.' The equivalent compression level LR file size is within 16KB of PS's file size, which is probably due to slight differences in in the file metadata.
    This pretty much confirms LR and PS use the same 'Baseline Standard' JPEG compression algorithms. The PS level 7 reduced quality is also seen at LR's level 54-61 JPEG Quality setting. Jeffrey Friedel mentions this in his analysis of LR's JPEG Quality settings and a reply from Brian Tao:
    http://regex.info/blog/lightroom-goodies/jpeg-quality
    Jeffrey Friedel's comment:
    One thing I find interesting (but don't understand) is that in the first example, the difference in file size between the  47〜53  quality and  54〜61  quality is considerable (49k to 66k bytes), while in the second example, the the same two levels of quality produces essentially the same file size. There seems to be some kind of switch in compression algorithm once Lightroom is at a quality setting of 54 or above that puts the emphasis on encoding the easily-discernible smooth gradients of the sunset example, and if they are lacking in the image, as with the reed-window-shade example, the attempt at extra quality fails, and the file size does not increase. That's my guess, but it's just a guess.
    Brian Tao's Reply:
    This is due to the downsampling (basically, a reduction in resolution) of one or more of the image channels before passing it to the actual compression routine.  Human vision is much more sensitive to changes in luminance (brightness) than chrominance (colour).  JPEG takes advantage of this by reducing the amount of colour information stored in the image in order to achieve higher compression ratios.  Because it is colour and not brightness that is sacrificed, this is called “chroma subsampling”.  Look up that term in Wikipedia for a far better and more detailed description than I can provide here.
    In a nutshell, Adobe products will use either a 4:4:4 subsampling (which is no subsampling at all, and thus full resolution) or 4:2:0 subsampling (both red and blue channels are reduced to one-quarter resolution before compression).  There is no switch to specify the amount of subsampling to use.  In Photoshop, the change from 4:2:0 to 4:4:4 happens between quality 6 and 7.  In Photoshop’s Save For Web, it happens between quality 50 and 51.  In Lightroom, you already noticed that something unexpected happens between 47-53 quality and 54-61 quality.  Guess what levels those correspond to in Photoshop?  6 and 7… exactly as expected.
    You can very easily demonstrate this by creating a worst-case scenario of JPEG chroma subsampling.  Create a small image in Photoshop with a pure blue (RGB = 0,0,255) background.  Now type in some pure red text (RGB = 255,0,0).  For maximum effect, turn off anti-aliasing, so each pixel is either full on red or full on blue. Zoom in to 500% or so for a clear view of the pixels.  Now save the image as a JPEG.  With the JPEG quality dialog visible, you will see a real-time preview of the effects of JPEG compression.  Start at 12, and work your way down to 0, one step at a time.  Watch what happens when you go from 7 to 6.  You can do the same with Save For Web and with Lightroom to confirm where they switch from 4:4:4 to 4:2:0.
    The file size discrepancy is more noticeable in the sunset shot because most of the information (relatively speaking) is needed to encode the gradual change in chrominance values.  There is virtually no luminance detail to worry about, except around the silhouette of the bird.  But in the photo of the reed window shades, the fine detail and texture and lack of colour result in practically no difference going from 4:4:4 and 4:2:0.
    Because of this hidden (and inaccessble) switch, I have been recommending that to be safe, one should never go below quality 7 in Photoshop, or 51 in Save For Web.  In Lightroom, this corresponds to quality 54.
    Hope this helps.

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