This is hard for me to test since I don't have a proxy to test it through. All I know is that under the seams it's using the .Net HttpWebClient classes which most likely inherit the IE settings but I can't be for sure. There is nothing that changed in the last few weeks code-wise and I've definitely not uploaded any new versions that would have automatically downloaded that would effect connectivity.
For those that are having this issues, please reply to this forum and give me your configurations and I'll see if I can find out what's going on.
-Joe