Coincidence or bad day - 2000 R1100RS

Went to start my bike the other morning and the engine would turn over a few times then stop. Hit the start button five or six times and the same thing but did ultimately start. Made it to work, and on the way home noticed a problem when idling at a light. It was like a piston would hit harder than normal every thirty seconds or so. It didn’t feel like it was happening while driving but continued the rest of the trip home when idling (about a 25 minute drive in traffic). Also noticed that my right blinker was blinking twice as fast as normal. Just moved to Tucson and didn’t know if heat could have a part in any of this. The temp on the bike has been fine so I’m doubting the 100+ temps are doing anything. The starting issue and the blinker I feel may be related, but I have no clue about the idling issue. Any help is much appreciated.

The fast right blinker could mean one of the bulbs is burned out.

So many bike problems can be traced to battery condition, I would start with that. Age of battery, condition of battery and battery terminal connections.
Once through those checks, the actual charging system can be checked for proper output.
Let us know how you make out.
OM