Silly me for not noticing the "Enable Resume Prompt" option in the config options of GB-PVR. That little check box enabled the main thing I missed from my Dish DVR. TV shows and videos can now be stopped and started right where I left off. Sweet.
Transcoding into WMV finally worked. I don't know why exactly, since I didn't change any settings or do anything differently. One day it didn't work, the next it did. I'm not questioning it for now. It changed a 1.5 gig file into a 320 meg file with only a slight change in video quality. Since I was looking for it, I could see the compression "blocks", but it wasn't distracting. If I didn't know what I was looking for, I wouldn't have even seen them.
I've now ditched my Dish DVR and have moved to GB-PVR exclusively. I love the system. Don't consider this project done yet, however. I still need to build a fancy box for the set up, install some plug-ins, and then build another front end for my other TV and network them together. This will be the fun stuff.