The Sample projects were great for testing purposes (they're much smaller and faster to generate!). After playing around a bit, I discovered the root of our issue may be the fact that we've inserted multimedia in our auto-sizing pop-ups (.flv video files). When we display the pop-ups in FireFox, they're so narrow that most of the video is cut off to the right. When I tried replacing one of the video files with a static image, the pop-up did re-size itself properly and it showed the entire image. So it seems that auto-sizing pop-ups work in FireFox with text and graphics, but not necessarily with multi-media.
To get around the issue, we've decided to display each of our videos in a new window (custom-sized pop-ups didn't work well either in cases where the help window was not maximized).
This issue doesn't seem to occur in IE. Auto-sizing pop-ups appear to re-size properly regardless of what they contain.