Why do Encore CS5 and Premiere Pro CS5 have intermittant Sync issues?

Question

I am noticing that Encore CS5 is "buggy" regarding sync issues with material edited by Womble and Corel Video Studio and I am guessing other programs as well?
In high definition I take AVCHD and  edit in Corel Video Studio.  If I leave the project as one single 42 minute segment and import this asset into Encore CS5, more often than not there are bad sync issues.  To get around this I have to divide the 42 minute project into approximately 6 smaller ones- Each smaller asset ends where I had done the editing.  Encore does not have any problems now with these 6 smaller assets.
In standard definition I edit in Womble and export as a MPEG2 Program.  Sometimes Encore has a problem with the asset sync and sometimes it does not.  (I am guessing about 20% of my assets end up with a problem).  The same asset if brought into TMP or brought back into Womble does not have any sync issue.  If brought into Premiere Pro CS5 it will exhibit the same behavior as Encore- If Encore has a sync problem, so will Premiere Pro.  So to get around this I then have to go back to the original womble file and break it up into smaller pieces, at every edit point I cut and export the smaller file just after the end of the transition I applied.  With a 6 hour project I may end up with dozens of small files to get around this problem- not very efficient.
Any ideas how to fix this or why Encore is so buggy?  Would moving the original assets around in Womble- example taking something that was at the end of the timeline and then moving it to the beginning cause these issues for Encore?   Or is there some other cause?
Encore CS5
Premiere Pro CS5
Windows 7 64 BIT
Quad core
2.4 GHZ clock speed
6GB memory
150 GB free space on drive
NVIDIA GEFORCE 8500 card

Answer 1

I've used VideoReDo in the past, which I believe has some similar strategies to Womble.  I found when I tested streams, that there were often problems in the source streams, and that the fix was not 100 percent.
You may also find such files that are not 100 percent the same length video to audio.
In any event, the possibility other than Encore being buggy is that the files you are bringing in have problems when Encore tries to validate them.  I'm not saying Encore doesn't have its problems, but clean mpeg files do not have sync issues ordinarily.
For some scenarios, I like your workflow (edit mpeg files in a frame accurate mpeg editor that is not retranscoding the whole file), but the results are often not consistent.
You don't say, and I would certainly look at, the nature of the audio stream you are using.  I can not tell you what the problems are, but some streams just do not edit well, even though they may play back okay in some players, but still have issues in Encore and/or Premiere.