I agree that this probably isn't a hardware problem - this is probably a Vista/Media Center/DVR-MS problem.
I have also had this problem with Heroes. Monday night both Heroes and The Tonight Show were bad for me. Heroes gave me a length of 8:14 and TTS said it was 9:11.
I downloaded that software to check out my metadata, but I didn't have any luck. There is a field named Duration, but it isn't editable.
For Heroes it gave the duration as '4943420000'. The Length property tells me the show is 8:14, which is 494 seconds. That seems to correspond to the '494' in the metadata duration field, but I don't know what the rest of the numbers would be. And like I said, the program won't let me edit this field anyways.
Matthew Toney - since you have supported tuners, could you post this problem in the "Ask Media Center Team" section of this forum? Jess usually seems quick to reply.