I have been fighting to convert both mkv files with x264/ac3 codecs and ts files with mpgv/ac3 codecs to wmvhd with the vc-1 codec. any programs ideas suggestions please help.
Windows Media Encoder is directshow based right? So it should just be able to re-encode them if you have dshow filters installed for playback.
Windows media player will play back the files, but media encoder gives me a giant middle finger when i try to use them as a source file.
Typical. MS invented dshow, but they can't make a decent dshow based encoder. You could try AVISynth with directshowsource(). You could then use WMNicEnc.