Hi ya Laurie :)...
How apt is the timing of this subject...I spent about 45 minutes on the phone to me old Mate Frank (MC Cruise), yesterday...10 minutes to sort my little conundrum out...the rest just general chit chat about shyte.
Anyway, I digress...Laurie, with the seat off, can you hear the relay (clicking / switching), with the cruise control computer when you apply the brakes (ign. on).?
Also spray some contact cleaner or such like in the switch for the MC cruise...the switch like ALL the OEM switches on the bike are not H2O proof, so I'm thinking of contact 'issue' within the MC switch.
The pulse you see means it's (the brake circuit), is receiving unwanted power from somewhere...the MC cruise as a the source on my part is a guess...the MC on your bike has an off the self computer, not the proprietary build of today...so bit of guess work on my part, but you have rightly considered the MC cruise.
I have just replaced all the incandescent lamps on the arse end of bike 1 with LED's, hence my call to Frank...Laurie, if my suggestion doesn't work, I am happy to phone him on you behalf, or call him yourself...most helpful...and best day will be this coming Wednesday.
Cheers, Dick :)