Yes it was all with the same server. Since it worked fine with FlashFXP but not IE/Windows I just assumed it might be the SP2 update. I'll try to find more info and post it here. <_<
Edit - I found out the server I was downloading from was Serv-U 5.0.0.11 and others have not noticed problems with other server programs. I question if it's just a problem with SP2 and Serv-U 5.0.0.11
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