Thank you so much for all the help! I now have this working- here is my analysis of the issue:
I'm just getting started with apache and this is my first Rewrite, so to focus on the regex my first rule was:
RewriteRule ^myfile\.php$ http://www.example.com/myfile2.php?100
So this worked, but did act as an external redirect, which I suspected since I had a full URL that mod_rewrite would assume to be external.
So for my next step I change it to how I reported:
RewriteRule ^myfile\.php$ /../myfile2.php?100
I read some misleading advice that said that targets should start with a leading "/", which makes sense 99% of the time, unless you are using relative paths- which I am. So I was operating under the false assumption that the target just needed to start with "/" as a rule. Thanks to lucy24's first response, I realized that was a problem.
The ?100 part of myfile2.php?100 is odd, but that is how that script works, it's actually a vbulletin CMS script which uses that notation a lot.
Anyway, with the malformed /../ I'm guessing mod_rewrite was just balking at the rule and ignoring the rewrite- but what I am also guessing is that the original rewrite that has the full URL was still in mod_rewrites rule processing list so it was still being applied- which made the /../ look like it was working, even though the original rule was doing the work. I'm not 100% sure on that but I changed my rewrite to:
RewriteRule ^myfile\.php$ /../myfile2JUNK.php?100
and it was still doing the same thing of going to myfile2.php?100, and not going to myfile2JUNK.php which obviously did not exist.
So as Dideved wrote, I should just be able to drop the leading slash- which made it legal and processed but unfortunately it didn't play well with the vbulletin script and the ?100 was basically being ignored.
I tired a dozen or so ways to get it to work but ultimately got this to do what I needed:
RewriteRule ^myfile\.php$ http://www.example.com/myfile2.php?100 [P]
Which is what I started with, but with the Proxy Throughput P flag, which makes it work as a dynamic mirror, per: [httpd.apache.org
I'm guessing this isn't the most optimized solution since I'm doing a proxy to my own site :) but I don't understand why the vbulletin script doesn't honor the ?100 without a full URL. None-the-less, this fits my needs for now.
As phranque suggest, I should enable the logging facility so I'm not working blind. I do have access to it but was hesitate to cause problems on the whole server.
Again, thank you very much for the help- you made all the difference!