I've been using FujiFilm DVD-Rs to burn DVDs. Here's my setup: DVD Decrypter, to get the movie to my HD. Then DVD2one to compress it. Then CopytoDVD to burn. When I put it in my stand alone, it plays like normal but during the movie there are several instances where there are 5 or 6 second skips!! These skips happen throughout the movie about 10 or 12 times and get cosiderably longer towards the end of the movie. Does this sound like a media problem??? I've used FujiFilm before without any problems, but I'm starting to wonder if maybe I got a bad batch of DVD-Rs.

Is the Fuji a rebadged Taiyo Yuden? What is the certified speed of the media and what speed are you burning at?

I'm not sure about about the discs being rebadged, but I have been burning at my burner's max speed which I think is 4x. The max write speed of the DVD-Rs is 8x, so I figured 4x would be ok. If I slowed it down to like 2x, do you think that would help?

You did everything absolutely the right way, burning a 8x media at 4x. It is safer.

Knowing the answer to the questions, my suggestion would be to try some other software for backups and see what will be the result.
Please, make a try with AnyDVD and CloneDVD2 or DVDShrink and Nero, burn at a lower speed (as you have done). Let's see what happens with skipping.

AnyDVD/CloneDVD2: www.slysoft.com
DVDShrink/Nero: www.dvdshrink.org