Memory is hazy... haven't played in TTPUB for awhile, but one
workaround I had employed due to some situation had been to
arbitrarily use an adjacent non-timepoint bus stop as the second
instance of a duplicated timepoint bus stop.
In the context of outputing schedule data, rounded to the nearest
minute, having the first instance of the timepoint bus stop reference
the second stop on the route (to the extent it was less than 60
seconds elapsed from the actual departure time)... or having the
second instance of the timepoint bus stop reference the second-to-last
stop on the trip (to the extent it would again round to the same
minute... or was close enough that publishing an arrival an extra
minute or two early wasn't of concern) resolved whatever issues I was
experiencing (and my recollection is that is was the repeated use of
an identical stop id on the same trip).
The GTFS data remains unchanged then, only the TTPUB configuration
tables need revising to arbitrarily swap which bus stops are used as
the published timepoints.