So the first problem turned out to be that the original version of the gif decoding library I used depended on JDK 1.2 to do the alpha compositing of those transparent partial frames. But back in the day, I didn't use JDK 1.2 features, so I removed that ability. I went ahead and switched back to the original library and it should work quite a bit better.
As far as the second problem, I'm not sure I understand exactly what is going wrong. As far as deduplicating frames, that is definitely intentional. If you have 5 of the same frame, you should end up with 1 entry in the frame pool and 5 entries in the sequence list. It /appears/ to be doing that properly, but it sounds like either 1) you don't want that or 2) it's not uploading that properly? Can you clarify a bit? By default, the deduplication is desirable, I believe ... If you really want each in a separate frame, I could maybe make a separate import that does not deduplicate or something?
jEmplode 60 is up there with the transparency fixes -- give it a shot and let me know if it works as you would expect now.