Well you know, in troubleshooting, the problem always exists in the last place you look. Sometimes I have to slap the forehead but hey you found something and that is what counts.
Anything now a days that controls power via a switching scheme is suspect to me. Motor controllers, power supplies, even those cheap power plugs for cigarette sockets raises my radar right off the bat when I spy them.
Maybe try one of those cheap shunt type solar controllers for a while until you can solve the interference thing from the fancier ones.