Strange quicktime codec export behavior

I was trying to make a movie from an image sequence using "export quicktime movie" today and had some odd results. The goal was to get the best quality for the least file size, and I needed alot of compression, so I tried many combinations of codecs and quality settings. The first oddity, was that the file size of the movie using "least" quality was higher than that of "low" quality for several codecs, including H264, MPEG and Sorensen 3. The second oddity was that if I scaled the movie during the export, I got a file that was the same size as the unscaled movie. If I scaled first in another program (ImageJ) and then made the movie, it was smaller than the unscaled. Comments?
BTW- the winner was Sorensen-3-low

Not sure what you mean. The codec used and quality setting have dramatic effects on the final file size. Just try rendering a movie with different quality settings and you will see the difference. I have done this many times and know it is true. I just never went to "least" before.
Some codecs have independent controls to restrict the data rates and set "quality" (i.e., reiteration of certain processes) while In others, the data rate may be incorporated into the "quality" control. The Apple Animation codec, for instance will increase the video data rate in proportion with increases in the "quality" setting but H.264 has independent/active control settings for each.
In more concrete terms, think of the data rate as the speed of a traveling car, the duration of your clip as the time a car travels, and the file size as the total distance traveled by the car. It is easy to see that a car traveling 100 mph for 4 hours covers a total distance of 400 miles while a car traveling at 50 mph only covers 200 miles. In a similar manner a clip having a total average data rate of 4.0 Mbps is twice as large as the same clip having a total average data rate of only 2.0 Mbps. Thus, if you really want to compare the differences in your file storage sizes, compare their their total average data rates and not their quality settings.
I scaled the movie from about 600x400 to 400x200.
Still not sure if you are referring to a change in the display dimensions or a change to the encoding matrix. This is important since it affects how different devices/applications deal with the content. Any clip can be re-scaled independent of the the encoded resolution. I.e., you can simple grab the lower right-hand corner of a QT player and drag it to change the clip's display dimensions. (Alternatively, you can change the properties window using QT 7 Pro). However, this action does not change the "encoded" resolution of the clip even if the scale change is saved in the file. On the other hand, if you exported or transcoded the modified file to video compression formats not having a "standardized" encode data matrix (e.g., like NTSC MPEG-2 or DV content has), then both the default scale and encode matrix are changed.
In the first case, where a file is simple rescaled, QT 7 would open with the display defaulted to the "Current Size" dimensions stored in the file and, if converted to a different video compression format, it would use the "Current Size" to set the target dimensions for the conversion. QT X, on the other hand, would not. It would ignore the "Current Size" setting and use the encoded dimensions for a "save" conversion.
To complicate matters, some conversion processes are device aware and may additionally restrict export/conversion dimensions. For instance, let's say I have a 640x360 file encoded at 29.97/30 fps. If I scale it to 1280x720 and then export the resulting file to the QT TV preset, I will end up with 960x540 encoded/display file. But, If I do the same thing to a 640x360 23.976 fps file, I would end up with a 1280x720 encoded/display file.
BTW: you do realize you are changing the 3:2 aspect ratio of the 600x400 file to 2:1 in the 400x200 file. (Or are we also taking about "cropping" as part of your work flow?)
In one case, I scaled the original data with ImageJ and then used the reduced size image sequence in Quicktime to export a movie... If I scaled first in another program (ImageJ) and then made the movie, it was smaller than the unscaled.
This is what I would normally expect in QT 7 Pro if the "scaled" clip has a changed "Current Size."
The second oddity was that if I scaled the movie during the export, I got a file that was the same size as the unscaled movie... In the other, I imported the full sized images sequence into Quicktime and set the smaller size with the size dialog during movie export.
You would have to provide more detailed information regarding your work flow here -- i.e., specific QT Player and/or target compressor and size settings if both options were available in your work flow.

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