Derek,
I'm using MCEBuddy 1.06b10 on Vista, and have a pretty fast machine (E6400 Core2Duo, 2 gigs RAM, ATI x1900xt GPU). I've mainly been converting from DIVX or DVR-MS to iPod 6th Gen compatible, to watch on an iPhone. Transcodes are relatively fast - maybe 15 mins for 30 minutes of video (not super-fast, but seems the norm for other transcoding apps I've tried). Tonight I tried to transcode a wmv file, and it took forever - like 1% after 15 minutes. I didn't let it finish. I'll try it on other wmv files and let you know if I can replicate the problem (i assume this is a bug).