Part #1:
1.) Do an uninstall of SH3. When the uninstall is complete, go into your control panel and verify that all files and folders have been removed from your C:/Programs/Ubisoft/SH3 area. Delete manually anything that may remain. Also make certain that any installed mods aren't auto-loaded upon bootup, such as SH Commander, which loads as soon as you run Silent Hunter.
2.) From the control panel, go to your My Documents and Folders folder, look for SH3 and delete any and all files remaining there.
3.) Click on RUN, type in REGEDIT and hit ENTER.
Scroll to HKEY_CURRENT_USER, highlight and expand the tree, scroll down to SOFTWARE, highlight and expand the tree again, scroll down to UBISOFT, expand the tree and scroll down to SILENT HUNTER III, scroll down to KEYS and highlight it. Now, on the right hand side, you should see two items, one is 'default', and the other should be called DiscKey_SH3...and to the right of that one should be your 25 character DVD code. Delete that entire line.
4.) Back up and find HKEY_LOCAL_MACHINE, and once again, scroll down to SOFTWARE, scroll down to UBISOFT and delete the entry.
5.) Delete the desktop icon/shortcut. Since this points to an old install, that pointer should no longer exist.
At this point, you SHOULD have all pointers to the original game installation(S) removed. NOW try a complete, fresh, clean install of SH3! DO NOT ADD MODS!
6.) Once the game is reinstalled, you should then be able to install the 1.4b patch. One thing here...make certain that you have the correct patch for your game, since there are four separate patches:
a.) On DVD bought in the U.S.
b.) On DVD bought in Europe (EMEA).
c.) Downloaded version for Europe (EMEA).
d.) Downloaded version for U.S.
Part #2:
As far as the entry that refuses to go away in your ADD/REMOVE software:
1.) Go to RUN, type in REGEDIT and hit ENTER
2.) Go to HKEY_Local_Machine/Software/Microsoft/Windows/CurrentVersion/Uninstall
3.) Scroll down to locate the Silent Hunter entry, delete the listing for Silent Hunter and EXIT.
The entry in ADD/REMOVE should now be history.