Before, either some random things would go into the .htaccess file or some lines would just be unsupported because of the web server change.
Can you check the .htaccess file for anything odd?
@Patrick.B and @caftpx10 were both correct; this was being caused by the .htaccess file in your "controlfunction" directory. A rewrite rule there was creating an infinite loop. I have commented out this line, and I no longer receive the Internal Server Error.