I did some testing, most seems OK, the error is caused by a to high threshold for the cutscene detection. Try to lower or use another cutscene.
Next to that I tried if I could tune the default comskip to work on your recording.
This comskip.ini based on the default version seems to do a good job without cutscenes. I inserted blank lines around the changes. Could you verify?
detect_method=111 ;1=black frame, 2=logo, 4=scene change, 8=fuzzy logic, 16=closed captions, 32=aspect ration, 64=silence, 128=cutscenes, 255=all
validate_silence=1 ; Default, set to 0 to force using this clues if selected above.
validate_uniform=1 ; Default, set to 0 to force using this clues (like pure white frames) if blackframe is selected above.
validate_scenechange=1 ; Default, set to 0 to force using this clues if selected above.
verbose=10 ;show a lot of extra info, level 5 is also OK, set to 0 to disable
max_brightness=60 ;frame not black if any pixels checked are greater than this (scale 0 to 255)
test_brightness=40 ;frame not pure black if any pixels checked are greater than this, will check average brightness (scale 0 to 255)
max_avg_brightness=25 ;maximum average brightness for a dim frame to be considered black (scale 0 to 255) 0 means autosetting
max_commercialbreak=600 ;maximum length in seconds to consider a segment a commercial break
min_commercialbreak=60 ;minimum length in seconds to consider a segment a commercial break
max_commercial_size=125 ;maximum time in seconds for a single commercial or multiple commercials if no breaks in between
min_commercial_size=4 ;mimimum time in seconds for a single commercial
min_show_segment_length=125 ; any segment longer than this will be scored towards show.
max_volume=500 ; any frame with sound volume larger than this will not be regarded as black frame
min_silence=20 ; Any deep silence longer than this amount of frames is a possible cutpoint
ticker_tape=0 ; Amount of pixels from bottom to ignore in all processing
logo_at_bottom=0 ; Set to 1 to search only for logo at the lower half of the video, do not combine with subtitle setting
punish=0 ; Compare to average for sum of 1=brightness, 2=uniform 4=volume, 8=silence, 16=schange, set to 0 to disable
punish_threshold=1.3 ; Multiply when amount is above average * punish_threshold
punish_modifier=2 ; When above average * threshold multiply score by this value
intelligent_brightness=0 ; Set to 1 to use a USA specific algorithm to tune some of the settings, not adviced outside the USA
logo_percentile=0.92 ; if more then this amount of logo is found then logo detection will be disabled
punish_no_logo=1 ; Default, set to 0 to avoid show segments without logo to be scored towards commercial
connect_blocks_with_logo=1 ; set to 1 if you want successive blocks with logo on the transition to be regarded as connected, set to 0 to disable
cut_on_ar_change=2 ; set to 1 if you want to cut also on aspect ratio changes, set to 0 to disable
delete_show_after_last_commercial=1 ; set to 1 if you want to delete the last block if its a show and after a commercial
delete_show_before_or_after_current=0 ; set to 1 if you want to delete the previous and the next show in the recording, this can lead to the deletion of trailers of next show
delete_block_after_commercial=0 ;set to max size of block in seconds to be discarded, set to 0 to disable
remove_before=0 ; amount of seconds of show to be removed before ALL commercials
remove_after=0 ; amount of seconds of show to be removed after ALL commercials
shrink_logo=5 ; Reduce the duration of the logo with this amount of seconds
after_logo=0 ; set to number of seconds after logo disappears comskip should start to search for silence to insert an additional cutpoint
max_repair_size=200 ; Will repair maximum 200 missing MPEG frames in the timeline, set to 0 to disable repairing for players that don't use PTS.
delete_logo_file=0 ; set to 1 if you want comskip to tidy up after finishing
output_framearray=0 ; create a big excel file for detailed analysis, set to 0 to disable
output_mls=0 ; set to 1 if you want MPeg Video Wizard bookmark file output
output_btv=0 ; set to 1 if you want Beyond TV chapter cutlist output
output_projectx=0 ; set to 1 if you want ProjectX cutlist output (Xcl)
output_demux=0 ; set to 1 if you want comskip to demux the mpeg file while scanning
live_tv=0 ; set to 1 if you use parallelprocessing and need the output while recording
live_tv_retries=1 ; change to 16 when using live_tv in BTV
standoff=0 ; change to 8000000 when using live_tv in BTV
cuttermaran_options="cut=\"true\" unattended=\"true\" muxResult=\"false\" snapToCutPoints=\"true\" closeApp=\"true\""
mpeg2schnitt_options="mpeg2schnitt.exe /S /E /R25 /Z %2 %1"
dvrcut_options="dvrcut \"%s.dvr-ms\" \"%s_clean.dvr-ms\" "
windowtitle="Comskip - %s"