Tom,
Just some miscellaneous thoughts on what you're experiencing...
First, your making good progress in ruling out possible causes. I believe at this point you can say: 1) your engine alternator and its charging circuit are ok, 2) both batteries are probably ok, and 3) the VSR is switching properly and thus allowing the charging of both batteries. This said, there are still some puzzling things going on.
Off the top of my head I can visualize two possible senarios that could cause what your experiencing:
Senario #1: the start battery was never drawn down however the VSR Start Switch did not make good contact (intermittent flaky switch).
- in this case when you switched to 'parallel' the engine started on the house battery.
- the 'clacking' you described by the VSR unit is troubling. Clacking is typically a switch engaging and disengaging, and should never occur on a properly designed and functioning product. The VSR circuit in this case would be designed to switch a 13.7V however with a 'hysteresis' of a tenth of a volt or so to avoid continuous engaging/disengaging when the voltage is right at the 13.7V threshold setting. If the 'start' switch is not making good contact, it is possible it is causing the clacking.
- a flaky switch would be a perfect 'electrical noise generator' which could explain why your VHF radio is acting up.
FURTHER TROUBLESHOOTING
If the starting problem reoccurs, measure the voltage on the start battery (now that you have a good voltmeter). Assuming the battery is ok, try switching the 'start' switch back and forth several time and try again. If you can get it to work, the problem resides in the 'start' switch portion of the VSR unit.
Senario #2 : something is drawing down the start battery when all the switches are 'off'.
- my BEP 716 VSR documentation does not specify a current draw when all switches are 'off'. I suspect it doesn't draw anything in this case.
- you may have several accessories that are connected directly to the batteries. The only way to find out for sure is to see what you can activate with the switches 'off'. Personally I have the Wallas, winlass, downrigger, cockpit bilge pump, and shore power charger connect directly to the batteries through fuses on my boat.
- anything directly connected to the start battery could be a culprit. By the way make sure you downrigger stays unplugged when not in use (although you had this problem before the downrigger).
FURTHER TROUBLESHOOTING
Now that you have a nice 4 1/2 digit voltmeter, use the current measuring feature. Use the 10 Amp position first before the 400 mA because both are fused at their respective values. With everything 'off' remove the ground cable on the negative post on the start battery and insert the leads of the meter between the post and the cable. If you read zero amps, repeat with the smaller scale on the meter. If you see any current at all on either position, your looking at a problem. Start disconnecting any wires on the start battery one at a time until the current disappears. Be careful not to turn anything 'on' when you have the meter connected. It's easy to blow the internal fuses in the meter.
Good Luck!