blueimp/jQuery-File-Upload — comment on commit 2e251218e578ebfa51c0018b7ce7f352ae723b2e
File:  line 0
By blueimp:

Well, it does definitely preserve the GIF and PNG transparency in my tests.
Maybe test the unmodified download package first to see if it works on your server setup.
If there is another fix needed on some setups, please let me know.