OK, this post may look a bit strange as I figured out a solution as I was typing up my problem. I will however leave the question below (and it's solution) for those who also may want to do what I did.... Read on....
I am able to run multiple instances of TB on my main windows machine by setting the environment variable MOZ_NO_REMOTE to 1. As long as I use separate profiles, everything is OK. Here is the problem.
I understand TB Portable only supports one profile, but I want to run both the portable TB (which has my personal emails and feeds on it) AND the main windows TB (which has my work emails). These of course are separate profiles with separate folders for the mail. When I try to start the portable TB (after the main TB is started from the start menu), I get an error that says only 1 instance of PORTABLE TB at a time. I therefore assume (because is specifically states PORTABLE TB) that the check is done from the launcher and not TB itself (which I assume would check the environment variable).
I'm sure the reason for this is that it would be bad (crossing the streams bad) for TB to start up a second instance and try to use the same profile as an already running TB. Since the portable TB only allows one profile, this is pretty important... Duh!
To get both TBs running at once is actually pretty simple (I feel stupid for not seeing it right away)... I just need to start the portable TB first, then the main TB (which looks at the environment variable).
OK, long post, I hope it helps someone else who needs to do what I did.
-Jeff
You need to use an INI file to set the advanced options. It's outlined in the readme.txt within ThunderbirdPortable\Other\Source. So, you're aware, it's only recommended for use on your own machine, isn't fully supported by us or Mozilla and will leave information behind including unread mail counts, etc.
Sometimes, the impossible can become possible, if you're awesome!