Check the sidestand switch first. Put the bike into reverse and back up, then put the sidestand down. The bike shouldn't back up. If this all works normal then check the clutch lever switches, one of them cancels the cruise and the other one is your possible culprit.
This could be as simple as a defective switch on the clutch lever or the sidestand switch, but it could be the reverse regulator assembly or wiring as well. Switches don't usually care much about how long you've been riding, but everytime you change gears you are working the clutch lever switch and maybe it's contacts are just dirty enough to cause this when it sets a while. There's 2 switches up there, one is for the cruise control system to cancel, and the other one is possibly your culprit. The cruise switch has a yellow/black wire, you will be interested in the other switch. Pull both wires(black) off of the switch and short them together, if the bike starts in gear with the sidestand up, you've found your problem.