Short story:
Java GUI is working again, I re-added the beamline crate to the 'slowc/HV_HALL_HRS' setup. Users are free to go back to the normal method of controlling cards in that crate (ie. using the normal 'hvgui_hrs' GUI).
Longer story:
It would seem the extra latency in the long (150') serial line was just enough to mess with the response time of the backend 'measure current' (MC) command for the 1461N cards. (And it seems only that command, the rest appear to return successfully...)
Anyway, the card returned nothing, the java gui filled the Meas_uA field with a NULL, and then freaked out when it tried to find how how to render a column full of NULLs.
I bumped the low-level delay up to 0.2s in hacuser@hacweb5:LecroyHV_shim/LecroyHV_FE/i2lchv_linux_brad.c' (was 0.1s) and the crate+GUI seem happy again.