What do you mean it won't recognize the tape? It won't play it back in your consumer camera?????
It really should be no different than playing back progressive footage in a consumer camera that only shoots interlaced.......the footage is already embedded into the tape, you are just playing it back and therefore the type of deck should have no bearing on what the computer reads during capture.
Now if you mean the timecode won't read correctly I have run across that with almost any footage shot from a different camera and played back, but unless you're producing a feature film, I wouldn't worry about the time code as you are only loading footage from one camera, not 4 or 5 that may be used on a movie set.

Are you by chance shooting progressive in HD? Maybe your big camera is removing the pulldown during the capture process and the small camera is not capable of this?