are you measuring the actual ac voltage at the patchbay (group outputs) with an rms meter? this would rule out converter calibration/meters/wiring/normals issues.
are the routing switches in good shape? all the ribbons that carry the busses between buckets are clean and seated properly? (also s10 on the lower buss board, which feeds the group amps?)
the alignment very well adjusts that signal though.
in direct, the channel sends its output only into the last stage of the group amp.
once you use the routing matrix, the group busses are passively summed on the lower buss card, and each group amp takes that signal off their respective buss (with direct NOT engaged). the group trim knob attenuates this signal, the trim pot adjusts the overall output (group and direct).
hope this makes sense, your problem will be in there somewhere