Ok, it's time to confirm that you've installed the mod correctly. It's possible that UAC and other random things are messing up the install to the point where it looks like it works but it won't.
There are multiple ways to install it understand but the following way is the most reliable.
Part one:
1. Download the Mod.
2. Right click on the FLMM Launch Shortcut and hit "Run as Admin". Do not double click or click from start menu, rather right click the item and select Run as Administrator. This is the critical step!!. If you don't don't this then everything will go wrong.
3. If you see any other discovery mod versions in FLMM, click the delete button. (Keep FLMM Running)
4. Click "restore backups" in FLMM. (Keep FLMM Running)
5. Double click the downloaded Discovery mod. (Keep FLMM Running)
6. Wait for the files to extract, and then activate the mod.
7. Play.
The run-as administrator bit is important due to the way FLMM and vista fight about access to the program files directory. When you load the mod into FLMM, FLMM needs to be running as administrator.
I think another way to install it is to install your entire FL game into "My Documents" or some other non system directory. Then FLMM should be able to happily update your FL installation - but I haven't really tested this.
Proud member of "the most paranoid group of people in the community"