Premiere Pro CS6 - Exported Video Longer Than Audio

Question

Hello all.  I've downloaded a series of tutorials from Groove 3 and have been using Premiere/Encore to convert them to Blu-rays.  Up until recently, I've had no problems with the workflow, but now I'm stuck and can't figure out what's happening.
The tutorials are broken down into individual video clips per chapter, AVC MP4 media, 30p.  Most of them are screen captures so they aren't in typical video resolutions, so what I've been doing is creating a new sequence in Premeire Pro (1280x720 59.94 or 30p, tried both) and brought the clips into the timeline.  I resize the video, add Encore chapter markers at the start of each clip, then export the sequence using the H.264 Blu-ray template with 1280x720 resolution.
The entire length of each tutorial varies - some are 90 minutes others are several hours - so sometimes I need to adjust the bitrate to ensure that I'm ending up with an .m4v that'll fit on the Blu-ray.
When I bring that .m4v clip into Encore as a timeline and preview the project, the markers start falling behind and there's considerable audio drift by the end of the sequence.
If I bring that exported clip back into premiere, I find that the video track is actually longer than the audio track, which explains the chapter markers/audio not lining up.  What I can't understand is why Premiere would export a video track that's longer than the audio track when everything lines up and plays back perfectly in the sequence timeline within PPro.
Again, I've used this workflow with previous tutorials and it worked fine, but I've not been able to fix this problem.  Even if I export a different container/codec out of PPro then convert it to .m4v in Media Encoder, I keep ending up with the same problem.
I'm thinking about making each chapter its own sequence and exporting each of them individually, then manually linking all of them together in Encore, but that seems like a pretty ridiculous workflow when everything should line up as is.
I had originally assumed it was because I was changing sequence settings when bringing the footage into PPro (I want the sequence to be in 1280x720, not the screen resolutions of the tutorial vids), but even when I ensure that the sequence frame rate matches that of the source videos, the exported media does not match up.
Ideas?

Answer 1

The tutorials are downloaded as a zip file then extracted; I don't actually screen record the tutorials while streaming or anything.  I guess I couldn't say if variable frame rate was used when they recorded the tutorials, but the media I have shows up as 30fps as opposed to some sort of non-traditional frame rate that often shows up when recording with something at a variable frame rate (like the stock iPhone video camera app).