Damping factor

>> Does the damping factor (control?) of an amp have any effect on that of a dedicated subwoofer amp connected via variable line out? <<

The damping factor is related to only two things: the output impedance of the final power stage and the impedance of the speaker, usually assumed 8 ohms for calculations. So NO, the damping factor of your power amplifier is not relevant when you are driving powered subs from a line output.

The only damping factor involved is that of the subwoofer amp. 

If you have a preamp feeding multiple amps you may be having an issue with impedance matching.  With solid state this isn't usually an issue.  Amps tend to have impedances in the 30-50kOhm range, and solid state preamps can usually handle 2-3 amps.. However if you are dealing with a tube preamp it may have issues.

The damping factor is basically the ability of the amplifier to control the driver, tightness. The higher the damping factor the faster the amplifier will be able the return the cone or diaphragm to the center or neutral position. An important specification for low frequency, woofer/subwoofer control, but can also affect low midrange drivers.

You are using two different preamps (the Bryston and the preamp section of the Hegel), and they have different sound signatures. Do this to isolate and hear the difference between the preamps:

1. Connect speakers to the PA-1 amp, and don't use the subwoofers
2. Connect Bryston variable line-out to the PA-1 and listen
3. Connect Hegel variable line-out to the PA-1 and listen

I would expect you to hear a difference, and it is caused by the Bryston and Hegel preamps having different sound signature. It follows that Bryston and Hegel should also sound different when connecting to the subwoofer amp,