12:10:57 2196 FairUse Wizard 2.8 log file
12:10:57 2196 1 processor(s) detected
12:10:57 2196 Directory set to : C:Program FilesFairUse Wizard 2
12:16:08 2196 Opening project, 91147 MB left on drive C:
12:16:09 2196 ------------------------------------------
12:16:09 2196 title=1, chain=0 (cells=19, duration=5674)
12:16:09 2196 ------------------------------------------
12:16:09 2196 chain 0, cell 1, vid 1, cid 1, from 0 to 118718, length 118719, fps=3, duration=300066
12:16:09 2196 chain 0, cell 2, vid 1, cid 2, from 118719 to 237673, length 118955, fps=3, duration=300300
12:16:09 2196 chain 0, cell 3, vid 1, cid 3, from 237674 to 356447, length 118774, fps=3, duration=300166
12:16:09 2196 chain 0, cell 4, vid 1, cid 4, from 356448 to 466978, length 110531, fps=3, duration=300366
12:16:09 2196 chain 0, cell 5, vid 1, cid 5, from 466979 to 569174, length 102196, fps=3, duration=300300
12:16:09 2196 chain 0, cell 6, vid 1, cid 6, from 569175 to 703602, length 134428, fps=3, duration=300166
12:16:09 2196 chain 0, cell 7, vid 1, cid 7, from 703603 to 831726, length 128124, fps=3, duration=300166
12:16:09 2196 chain 0, cell 8, vid 1, cid 8, from 831727 to 950709, length 118983, fps=3, duration=300300
12:16:09 2196 chain 0, cell 9, vid 1, cid 9, from 950710 to 1054401, length 103692, fps=3, duration=300166
12:16:09 2196 chain 0, cell 10, vid 1, cid 10, from 1054402 to 1173193, length 118792, fps=3, duration=300300
12:16:09 2196 chain 0, cell 11, vid 1, cid 11, from 1173194 to 1280152, length 106959, fps=3, duration=300166
12:16:09 2196 chain 0, cell 12, vid 1, cid 12, from 1280153 to 1410774, length 130622, fps=3, duration=300166
12:16:09 2196 chain 0, cell 13, vid 1, cid 13, from 1410775 to 1545041, length 134267, fps=3, duration=300300
12:16:09 2196 chain 0, cell 14, vid 1, cid 14, from 1545042 to 1663485, length 118444, fps=3, duration=300166
12:16:09 2196 chain 0, cell 15, vid 1, cid 15, from 1663486 to 1782651, length 119166, fps=3, duration=300300
12:16:09 2196 chain 0, cell 16, vid 1, cid 16, from 1782652 to 1901410, length 118759, fps=3, duration=300166
12:16:09 2196 chain 0, cell 17, vid 1, cid 17, from 1901411 to 2020185, length 118775, fps=3, duration=300166
12:16:09 2196 chain 0, cell 18, vid 1, cid 18, from 2020186 to 2124778, length 104593, fps=3, duration=300300
12:16:09 2196 chain 0, cell 19, vid 1, cid 19, from 2124779 to 2219006, length 94228, fps=3, duration=274233
12:16:13 2196 _IndexProgress() : Loading program chain index...
12:16:14 2196 _IndexProgress() : Grouping sections by video type...
12:16:14 2196 _IndexProgress() : Synchronising streams...
12:16:14 2196 =======================================================================
12:16:14 2196 AC3 Audio 0 = Stream 0
12:16:14 2196 =======================================================================
12:16:14 2196 Audio track found: 00: English, AC3, 192k/2.0
12:16:14 2196 =======================================================================
12:16:29 2196 -----------------------------------------------------------------
12:16:29 2196 Encoding settings :
12:16:29 2196 -----------------------------------------------------------------
12:16:29 2196 _TranscodeProcess() : Encoding part 1 of 1
12:16:29 2196 _TranscodeProcess() : Starting pass 1

Does it happen with all DVDs? Have you tried multiple codecs? (XviD and H264 for example)