Rotation problem after editing in Photoshop

Question

I'm using Lightroom 1.3 and Photoshop CS3 with all the current updates. This problem was the same in LR1 and PS CS2.
I have a mix of orientations in the JPEGs in my library - portrait and landscape. When the photos are imported into LR they appear correct. If I select a bunch of them, open them in PS (using Edit in Photoshop > Edit Originals), run a noise filter, save them, and then go back to LR, the previews for the portrait images are rotated so that all the previews show as landscape.
The portrait images display correctly (except for the fact that they have been rotated) in the Library module - both grid and loupe view). In the Develop module, the image aspect is displayed portrait but the image is as a distorted landscape - the image is rotated and then distorted to fill the portrait oriented space. In the Print module, that same distorted image is fills the portrait oriented page. To be clear, instead of a portrait image appearing in the correct orientation on a portrait page preview, the image is rotated 90 degrees and then stretched to fill the page.
There is a badge on the preview indicating that the metadata is out of sync with the file.
If I rotate the image in LR, the badge goes away and the image appears portrait and undistorted in the Library module's grid and loupe views. The Develop module show the portrait image in the correct rotation, but has been stretched to a landscape aspect. The Print module shows that distorted image rotated to fit the portrait page.
The only way to correct this is to "Read Metadata from file". This resets all the orientation information so that it displays correctly in LR, but all the tags and IPTC information gets erased.
This is most of the reason why I was writing all the metadata into to files until now. I would write the metadata before editing in PS, do my PS edits, and then back in LR I'd "Read the Metadata" from the files to set everything correctly in LR. But of course now that I'm working with Leopard I get screwed if I do this because my files will crash the Finder.
To top it all off, I've run into the "...cannot be saved because the file is in use" problem with some files I opened last night.
Clearly none of these issues are being addressed in Adobe or Apple's updates. Is there a reasonable workaround that will let me:
1. set metadata and tags and know that they won't either get lost or cause problems
2. have image orientation respected and displayed correctly
3. not crash any of the three critical applications on this computer - Lightroom, Photoshop, and Finder.

Answer 1

I really appreciate your explaining this Jao.
I'm going to explain how I got into this situation, in the hopes that it may prove useful to someone (I'm looking at you, Adobe) who wants to understand how the app is being used in the real world.
So as not to break up the narrative, let me just say that I'd be happy (ecstatic, actually) if I could use Lightroom for my entire workflow, but the noise reduction filter in LR is just nowhere near as good as NoiseNinja. (A problem shared by LR, PS, and Aperture.) If I could run NN from inside LR, that would rock.
Oh, and I shoot JPEG because I shoot live events where the lighting is usually crap and I need to be ready at any moment for something interesting to happen. Shooting RAW would be nice, but it's too slow and takes up way too much space.
So here's what I do, (hopefully edited to make the reading non-tedious)
1. import all photos from source (usually memory cards)
The photos go onto a drive reserved for photos. I shoot events, so everything is organised by date-event. On import I set filenames (date - event name - time stamp.jpg) and keywords.
2. cull
They get marked "1" (irretrievably useless, to be deleted), "2" (keep just in case), "3" (decent shots), "4" (photos that I want to show to other people), or "5" (this is one of my best this year). Delete the "1"s.
3. select 20-30 "picks"
I create a folder within the event folder called "Picks" for these photos. Then I duplicate that folder as "Originals"
In doing it this way I can protect myself if I need/want to change my cataloguing application. I'm on my fourth one at this point (Lightroom) and while I am generally finding that LR is meeting my needs more than anything else I've tried, I've been burned in the past (how many of us have regretted letting Aperture put all our photos into an incomprehensible database/folder hell?)
The Picks/Originals structure makes sure that the originals never get touched (because it doesn't show up in LR) and I can quickly find the Picks.
I -was- writing the metadata to the files so the ratings, keywords, and IPTC info was where it should be - attached to the photo. I've stopped doing this for the time being until this whole Finder-craching debacle is corrected.
So why am I not using LR's built "Edit - Copy"/stacking function, which more or less duplicates my process?
Well part of it was my own dumbness - Aperture made the edited copy/variation a Photoshop file, which ballooned my collections with staggering speed. I'm not sure if LR used to do the same thing, or I just made the assumption. My mistake.
The other part of the problem is just the simplicity of having an Originals folder that is effectively ignored. Using LR will mix the "-edited" files in with originals, which is not as efficient or elegant a solution, but I'll give it a whirl.
Thanks for your suggestion. If giving up my Picks/Original process solves the rotation problem then perhaps it's a fair trade.
Still, it seems that the right hand is somehow oblivious to what the left hand is doing in the whole PS/LR thing, and that it ought not work that way.