Only if you are running multiple copies of our tool at one time. I guess you could do that, but user beware. I just select between serial ports when I am programming multiple boards.I see a conflict "Our tools write into %temp%\Coridium any log files......" --maybe two different APPS are writing the log file.
As for Program Files being protected, anyone who has tired to write/rename/delete in there knows you need Admin priveledges, so if you need to save the Tcl log, which I have never looked at in 12 years, you need to save it somewhere else. As that Tcl log just has what is in the popup, and for me to debug it I usually need more context like a screen shot.