When I looked in my Silent Hunter III root directory c:\Program Files/Ubisoft/Silent Hunter III, besides the program JSGME.exe, I found all the extracted folders along with the tga files and readme files for all the instalations I did on Apr 11 and Apr 13. These extracted folders were also in the MOD folder. I don't think this is the way it is supposed to happen.

Am I correct on this assumption? I knew something was wrong when I played SH3 yesterday because none of the patches showed up in the game and the things that were supposed to be added to the game were not there and nothing was happening in the game. So, that's when I started reading the instruction sheets that came with each mod I installed. What I did next was to manually put the files where there were supposed to be because they where not there, they were in the root directory. That's when the program crashed after trying to load my career and I received the Windows' error reoprt. Now I'm not that great on deciphering those reports and I did not send them to Microsoft. I just clicked on the "do not send" and then the SH3 quit and I was back to my desktop theme.
So, what I plan to do is, first remove the files I installed manually, and put the backup files back in. Then I will run JSGME.exe which is my generic mod enabler v 1.4.0.49 and remove each mod from the activated list. I also noticed that I have RUb1.45 which was installed on April 4th. On Apr 4, it seems that all those mods (6 of them) worked when running SH3, but the mods extracted after that date, did not work when running SH3. I think because the files extracted in two places, the root directory and the MOD folder.
So, first thing I am going to do, while waiting for an answer from someone to clear this situation up is to start removing the mods using the mod enabler and move the activated from the right back to the left side. Them I will wait for a response from someone.
Robert