64bit sync issue

[synapse46]

I was previously using 095 and updated to 096 64bit and get the below output continoiusly repeating and video seems to be garbled after a minute or so. The 32bit 096 seems to work fine. I'm using win7 and the following command.
"C:\Program Files\Handbrake\HandBrakeCLI" -t 0 --main-feature --markers --subtitle-forced scan --no-dvdnav --preset="AppleTV 2" -i D:\VIDEO_TS\ -o c:\temp\movie.m4v

Encoding: task 1 of 1, 0.68 % (22.94 fps, avg 12.78 fps, ETA 03h24m26s)[16:42:42
] mpeg2 tag botch: pts 8141133, tag pts 7798791 buf 0x0000000000000000
[16:42:42] output track 1: ac3 in sync after skipping 6144 bytes
[16:42:42] sync: adding 149 ms of silence to audio 0x80bd start 8107200, next 8
093760
[16:42:42] mpeg2 tag botch: pts 8186178, tag pts 7851343 buf 0x0000000000000000
[16:42:42] output track 1: ac3 in sync after skipping 3072 bytes
[16:42:42] output track 2: ac3 in sync after skipping 6144 bytes
[16:42:42] output track 2: ac3 in sync after skipping 3072 bytes
[16:42:42] sync: adding 160 ms of silence to audio 0x80bd start 8107200, next 8
Encoding: task 1 of 1, 0.69 % (22.94 fps, avg 12.78 fps, ETA 03h24m26s)
Encoding: task 1 of 1, 0.69 % (22.94 fps, avg 12.78 fps, ETA 03h24m26s)[16:42:42
] mpeg2 tag botch: pts 8231223, tag pts 7896388 buf 0x0000000000000000
[16:42:42] output track 1: ac3 in sync after skipping 3072 bytes
[16:42:42] output track 2: ac3 in sync after skipping 3072 bytes
[16:42:42] sync: adding 128 ms of silence to audio 0x80bd start 8190720, next 8
179200
[16:42:42] mpeg2 tag botch: pts 8276268, tag pts 7941433 buf 0x0000000000000000
[16:42:42] output track 1: ac3 in sync after skipping 7680 bytes
Encoding: task 1 of 1, 0.69 % (34.06 fps, avg 13.34 fps, ETA 03h15m47s)[16:42:42
] mpeg2 tag botch: pts 8321313, tag pts 7986478 buf 0x0000000000000000
[16:42:42] output track 2: ac3 in sync after skipping 7680 bytes
[16:42:42] sync: adding 160 ms of silence to audio 0x80bd start 8239680, next 8
225280
[16:42:42] sync: adding 128 ms of silence to audio 0x80bd start 8190720, next 8
179200