The SOP line is not used. The EOP is crucial....The EOP is part of the clocking table and the state-machine ouputing clocks uses it to re-start clocking at the strart of the table. If EOP were not configured then the clocking and converting (coadding)components would get out of sync with the array size.
I added an EOP to the clock table and the rolling stopped :) The key line added to the .btg (pasted below for reference) is 'and EOP !1 H 1', and it tells the btg app to strobe the EOP bit for one time period at the end of the file.
TABLELEN 1361920
TIMEPER 1 # ca. 1 microsec per table entry
NBITS 21 # 32 max
VrstOff L & #set low and stay low
# CLK2:
pC1 H ( 5 5 4 6 ( 4 6 )128 4 26 )*
# CLK3:
pC2 H ( 5 10 4 6 ( 4 6 )127 4 31 )*
# CLK4
VnCol L &
# CLK5
VnRow L &
# CLK6
VpRow L &
# CLK7
prston L 1305 ( 25 2635 )*
# CLK8
-SOP L &
# CLK9
-EOP L &
# CLK10
pRowOn L 1305 ( 25 2635 )*
# CLK11
VRowOff L &
# CLK12
VggCl L &
# CLK13:
pR2 H 5 1327 ( 1329 1331 )*
# CLK14:
pR1 H 5 5 1321 ( 1331 1329 )*
# CLK15
pRefEnable L &
# CLK16
VnpwR L &
# CLK17
VnpwT L &
# CLK18
VnStat L &
Z19 L &
Z20 L &
# CLK21
-CTC L ( 13 1 4 1 ( 4 1 )253 4 1 41 )*
and EOP !1 H 1
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