I noticed then that the log book and my saved files were from my boxed version. It didn't actually try and reinstall the whole program but I had to click each window before it would eventually start the actual program. I ran FX10SE several times and each time it went through loading the install and other files. FX10 Uninstall does not erase them and shouldn't.
The logs, added aircraft and Saved Flights were still on my hard drive. I was going to reinstall it but instead I installed FX10SE. I had uninstalled it do to some problem causing it not to load. When I installed FX10SE my boxed version FX10 was not installed.