It's usually helpful to mention the version you're using, but I've since similiar things happen with the last three versions of PP -
Since your issue is occuring in the encoding process (and not the burning), the two most likely causes are:
1. A blank space with no video.
2. An insert that sliced and left a single frame pushed to the right of the preceding clip.
First thing I'd do is check the end of all sequences to ensure that no sound track exceeded the video track by even a single frame, although this can occur anywhere in the sequence, I find it most often at the sequence end.
The second can be very hard to find, since you're looking for a single orphan frame, but PP's shortcut keys can help. Go into each sequence - expand just enough to be able to diferentiate small clips - and use the Pg-Dn key to move from clip to clip. If you do that and one time it doesn't look like the timeline indicator has moved, look more closely - this could be your orphan.
As KBVP pointed out, the percentage indicator gives you a rough idea where to start.
Good luck!