New to mods and confused!

[Floater]

I've been playing SH3 now almost since it came out, but never got round to installing any mods for fear of messing up. Yesterday, I decided to "push the boat out" and see what I've been missing out on. It's not worked out well so far.

Here's what I've done, testing after each stage:

- Reinstalled SH3 from scratch; upgraded to official 1.4b
- Downloaded JSGME 1.3.3.41 and installed
- Ditto for IUB, which I thought I'd try first; installed it into MODS folder
- JSGME picked up 7 different mods (ClearWater, etc), which I enabled
- SH3 did a CTD on loading missions
- Disabled IUB, tested, all seems OK
- Installed RUb1.45 into MODS; it appeared as a single entry in JSGME
- Enabled RUB1.45
- Found my SilentHunterIII root folder full of folders and files!
- Disabled RUB1.45
- Root folder still full of folders and files
- Maybe that's how it's supposed to be? Reenabled RUB1.45
- SH3 CTDs
- Disabled RUB1.45
- Removed added folders and files from root folder
- SH3 works again

What's up? I'm baffled! My install is pretty standard stuff, except that it's on my I: drive (ie my HDD - my C: drive is a card reader, blame the guy who set it up), but other than that it's a vanilla WinXP P4 system.

Please help a frustated man who is full of woe!