That's interesting - are those "official" covers from Garrett or after-market? I never knew they made them. I just sent in my orange one yesterday for warranty repair (would beep constantly when used underwater and I had to take the battery out to get it to stop...same thing happened to a friend of mine's the same day at the same location. Apparently we were in some "special" water.) Are those covers there also waterproof, and have you noticed any decrease in sensitivity when using them?
My big complaint about the Garrett pinpointers is how much of a pain in the butt it is to change sensitivities. I have the Minelab pinpointer also, which has just a simple +/- switch for sensitivity, but i feel like the highest sensitivity on that still isn't as sensitive as even the minimum on the Garrett.