Timecode oddness with mp4 video

Time Code is a tricky thing.  It use to be a number burned into each frame,  but guess what?  We don't use actual frames anymore. 
 
Maybe your TC is not 23 fps.  Try other formats.  If your TC starts out correct and then drifts farther and farther away over time, there is a mismatch in TC.  If it is off 2-3 frames at a random point, then back to correct latter on...and so forth,  that is normal and just 2 systems not agreeing where a frame starts and stops...cause there really are no frames.   If TC starts correct and then at some point becomes 3 frames off everywhere it is most likely that those 3 frames where skipped by the system when generating the TC.  I use to seen that a lot.
 
I work with a lot of TV and starting @ 00:00:00;00 is something we all avoid 'cause it causes a host of problems.  I always burn my own TC to look at along with what the editor sent, so when I'm scoring to pic I can see the Editors TC,  TC generated from Sony Vegas and Sonar's own TC.  I generate an AVI file to work with cause you never know what is going to be up with Quicktime or .mp4 files.  If there is a TC conflict I just keep working and use Sonar's TC to guide my edits (Rarely does Sony Vegas and Sonar's TC conflict) and then have a conversation with the editor and the sound mixer just to avoid any issues.  Computers hold time very well and any sync issues are easily fixed.