Shaun, found the following after a good bit of searching on Google, at sonytalk.com regarding ingesting TM 900 files. See if any of this helps.
The problem that you are having is not new with these cameras. There is a file size limit that splits them in to segments. When the clips are put on the time line of your editor, and merged together, and played back there are dropped frames at the beginning and at the end of the clips, which seems to be the problem you are having. There are two methods that avoid the splitting of clips with no drop outs, one is to use the software that comes with the camera (HD Writer) or using a Dos Batch Binery command.
Here is a link to the discussion of this problem: (Sorry about no hyper links)
http://www.dvinfo.net/conf/avchd-format-discussion/113083-canon-vixia-hg10-2gb-file-limit-headache.html
Here is the method of doing a binery command:
http://www.dvinfo.net/conf/showthread.php?t=84003
