I talked to Alex today and had two things fixed:
First the maximum length of filter names (in the foton C1SYS.txt files in /chans) has been increased to 40, from 20. This does not increase EPICS channel name length (which is longer than 20 anyways).
This should prevent running into the case where the model doesn't complain when compiled, but we can't load filters.
Additionally, we modified the feCodeGen.pl script in /opt/rtcds/caltech/c1/core/advLigoRTS/src/epics/util/ to correctly generate names for filters in all cases. There was a problem where the C1 was being left off the file name when in the simulink .mdl file the filter was located in a box which had "top_names" set.