I know this isn’t an in depth answer (I’m at work and can’t really test any code) but, maybe you need to look at directly creating hooks for your upload – which should mean that the flash uploader will act as you expect.
The hook for the flash loader is: pre-flash-upload-ui
You can see where this hook appears here:
http://adambrown.info/p/wp_hooks/hook/pre-flash-upload-ui
Some other stems/hooks to look at are these:
- post-html-upload-ui
- post-plupload-upload-ui
- post-upload-ui
- pre-flash-upload-ui
Also regarding the media uploader and $GET in one of your conditions – I think $REQUEST is preferred.
Sorry for the vague answer but inspecting these hooks may help you find a solution to your problem – hopefully I’ll be able to expand and test later tonight and help out a bit more
Craig