You should know that some Cyberhome Models are very sensible according to min Bitrate in case of VBR encodings!
So maybe the one stream got padding in TmpgEnc enabled and the other stream not.
But you should build your own Compatib.Disk Image by encoding some identical source 1 minute clips based on diff. resolutions and also these diff res. in diff min Bitrate settings and padding on/off.
This would end up in 20-30 muxed clips, very easy to author using VCDeasy or Nero, so u can choose via menu the one to test and know which one u are testing as the disk then got many streams