The FW problem is not resolved - but the usual work-around worked also this time: reboot everything. Power cycle. Then the 55536 error code went away, and the script to set focus and take images and save data worked as intended. This time I believe the results because the collected fluxes at the same exposure time through different filters depended on the filter in a sensible way:
Filter median flux
The focus is still hard to determine from data like this, though:
It seems to me that the radius measurement may be useful, and the SD method. Not all filters can have their focus determined from the above - wider limits must be set, and I will do that to get a clearer 'peak' answer.
The above is the result of a single run through all filters so the occurrence of 'double tracks' in some places is really mystifying.
It remains unclear why the FW did not move, but it is probably related to that 55536 signal. The other error code was a reference to the dome not finished with a home seek. Not sure if that influences the ability of the FW to move??
None of this explains the previous problem we have had with VE2 alone - in a sequence of good B,V, VE1 and IRCUT VE2 was suddenly out of focus, and then back in. Hmm.