As stated in the official changelog, version 0.9.5.4 contains strengthened security checks for various formats, including more rigorous validation of Ogg Vorbis files.
I had a similar problem as you with some Vorbis tracks extracted from a movie in Matroska container. As I learned, the cause was "mkvextract" writing invalid granule positions to the Ogg file. While this jitter was inaudible because of MDCT windowing, the files were wrongly decoded because of this (and half a second shorter in the end!).
The Ogg Vorbis specification says decoders should handle this kind of errors gracefully, but I'm glad the new foobar2000 version refused to play these files so I could fix them.
I've made myself a simple command-line program to do this. You might try it on one of your problematic files and see if it helps:
revorb.exe (72 KB)
CODE
C:\Data\src\xiph>revorb
-= REVORB - <yirkha@fud.cz> 2008/06/29 =-
Recomputes page granule positions in Ogg Vorbis files.
Usage:
revorb <input.ogg> <output.ogg>
C:\Data\src\xiph>revorb "BCW title music (eng).ogg" "BCW title music (eng).fixed.ogg"
C:\Data\src\xiph>