Selenium RC + Firefox profile behavior different than Manually Opening FF

I'm currently using Selenium RC to run java based TestNG tests via Eclipse IDE. I'm running into a problem which I had not seen before.

In my testing I use a firefox profile that has certain certificates added, plus an add-on that is used to remember certificates etc. When the tests are run I believe it uses a copy of the profile, but any changes made during the test session will be lost because it is just a copy. So to set-up the base profile I have to open it manually, make whatever changes are necessary, and then close it.

When running the tests, selenium RC is called with the specified Profile using the option -firefoxprofiletemplate. This has always worked in the past. Recently however I have noticed that although the correct profile is being loaded, the behavior of the profile is not as expected when the tests are run via selenium RC. When I run the automation, the FF add-on's window pops up, and I get certain errors on https pages related to certificates not being accepted, which leads to pages loading without media (no css, images etc).

If I try to correct this by manually opening FF with the exact same profile, none of this happens. The add-ons window does not show, because I specifically disabled that behavior- and I get no problems loading the same https pages as in the automation. Does anyone know what might be the cause of this? do the certificates get added as a certain user and the automation is maybe running as another user or something? I tried running the .bat file that kicks off RC as administrator, but that didn't work either. I just have no idea why the same profile would be acting differently when opened via different methods... I've never seen this problem in the past.

Right now I'm running in FF 3.6.22 and RC 2.5 Any help would be appreciated. Thanks!