I don't know what method you used to perform the transcoding but if you remove a file, gbpvr has a feature to remove recordings with missing files from the recordings database. Is it gone from pvrx2's ready list as well? I've never transcoded anything but there are a few places on the wiki that explain transcoding if you search.
I've never tried XRecord's transcoding feature but I assume it's buggy and fixing it is already on my todo list but at the bottom since nobody has ever asked for it since I took over XRecord.
2 Hauppauge PVR-150's, Celeron 2.93GHz, 1GB RAM, 1TB Maxtor HD, Cooler Master Cavalier 2, Radeon HD 2400 Pro, gbpvr 1.1.5 Blue Skin