I guess it's already late, but I think I had the same problem as you. Civ3 Multitool was working fine for a while, later on the program didn't load. There are no errors, no crash, it just won't load.
What I found:
In the task manager it was using one processor core 100%. Stopping the process & restarting the app didn't help.
Tried cleaning system with ccleaner - no success
Tried disabling and re-enabling winxp compatibility mode - no success
Manual checking of registry for any error - no success
When I checked the installation directory, I spotted that logs.dat file is over 1GB!!!
- nice work from such a small program... Deleting the logs.dat solved the problem, the tool ran again.
Hope this helps for someone having the same isssue.