Not sure what your referring to. I need exact step by step explanation of what your trying to say.
If an image is in the data directory then it is in your gallery. That comment alone is very confusing because if the image is truly in your data directory it has been processed into your gallery or it would not be there. An image is only moved into your data directory after it is processed meaning the info has been added to the database and it is moved from the uploads directory to the data directory which is the final resting place of the final image.
I can only guess your trying to say your flash uploader is not working but regular uploads work?
Chuck S Gallery - Omegatron Gallery
I did a little test uploaded 7 2mb each files and they where all processed. The flash uploader does not work on all servers and issues with it would not be endemic of a specific version of the gallery. Like if your server has mod security turned on then flash uploads would not work.
Let me know exactly what your problem is so I can respond accordingly. The site I am showing you is my clean 8.21 install that I do testing on.