Sounds Like a codec Issue to me...If you have a Bunch of codec Packs installed then you will eventually run into these Types of Problems as they install many conflicting Codecs....
I can decode every Popular AVI format there is all with Just One codec which is "FFDShow Decoder" which is all you need to Watching and decodeing Video Files....
If Sorting out your Codecs doesn"t solve your Problem then I suggest that you Run TMPGEnc and go to "Options" to "Enviromental Settings" to "VFAPI Plugins" and Raise the Priority of the "Direct Show Multi-Media File Reader" to "2" and then Try Loading in an AVI file and you shouldn"t have any problems.....
In MainConcept you Might try Fooling arround with the Import Modules...If you go to "options" to "Import Modules" then you can Try Disableing and enableing different ones to see if it helps....
I use Both Encoders Fairly regular and I never have Problems with it Not supporting file Types, i can even Get TMPGEnc to accept MP4 files and AVI files with Dolby AC3 audio.....
If it is a variety of codecs installed, I would suggest uninstalling and go to the software download tab above and browse on over to "CODECS", find the K-Lite codec pack, download and install. I used MainConcept routinely with no problems. Still looking for time to examine TMPG.