I don't know if this was caused by the fix in r451, but I was attempting to force the fps of an FLV file to 24000/1001 and the resultant MPEG-2 file had its audio sync skewed (as did the script itself when played in a media player) - since I didn't know if maybe it was a problem with HCenc 0.26's pulldown flagging, I removed the flags with DGPulldown and remuxed, but the desync was still there. When I've used the same build on FLVs I'm forcing to 30000/1001, there's no desync (however, the 29.97 stuff is H.264/AAC, the skewed 23.976 is VP6F/MP3).
The FLV file in question was reported as 23.976 Constant fps by mediainfo, but using FLVExtract to dump the video, audio, and timecodes output the video fps as 23.444. So I used avi2tc and inserted null frames into the video to make sure it equaled 23.976, and then loaded it and the decoded PCM audio track using AVISource. No sync issue. Loading that same corrected AVI file with FFVideoSource results in the desync also seen in the FLV.
On a related note, I've been getting crashes at the end of encoding using HCenc (both 0.25 and now 0.26). It reports that it's ffms2.dll that crashed, but this doesn't happen with other programs, which makes me think it's HCenc. On the other hand, rolling back to the vanilla 2.14 official build results in no crash. But my own C-interface compiles (also vanilla, not -mt - at least not before that got merged) all exhibit the behavior, even with revisions close to when 2.14 was tagged. I seem to recall the official 2.15 vanilla build crashing too, but can't say that definitively.