A short time after turning on the cruise control in my 2008 Subaru Impreza manual hatch the engine seems to stutter and the cruise control turns off, the dash light flashes and the vehicle dynamics control warning light comes on. The dealer reset it on their computer and told me it was a catalytic converter issue, but the car hasn't missed a beat and no lights have come on at all when I've driven it without using the cruise control. I believe it could be an electronic issue given it doesn't occur unless cruise control is on.
If it is still doing it having been worked on by the dealer it's a fair bet that it is an electronics issue as you suspect. It could be a faulty sensor or a bad connection.