I just tried logging in with IE11 (Win7) and had no issues.
I suggest that you remove all cookies belonging to project-gc.com, and if that doesn't work, from geocaching.com as well. Our experience tells us that it's some issues with the geocaching.com -cookies. Somehting we are not in control of, and probably an issue with Groundspeak. However, since we have never managed to reproduce the issue, we haven't been able to investigate it.
For settings, I don't know, but nothing special. Default should work well. The IE11 I tested in is a clean install that I use for the single purpose on testing the Project-GC web with that specific browser. As how the authentication works, your browsers isn't really aware of that you are matching two sites together.