What kind of insertion loss do you have through the cans individually? Once of them may have developed "tin whiskers" causing weird stuff to happen. I've even cracked the cheap pot-metal SO-239 connectors on the cans causing horrible losses, too.
Also, how much power is your exciter driving the Henry with? If you're underdriving either amp (internal repeater PA or the Henry), I've seen spurs and 2nd harmonics go crazy. Also, check the coax between the repeater and the amp. You can use your HP SM on tracking gen to do this (just insert it between ANT and GEN). If it has 3-6DB loss (and I've had teflon jumpers get this lossy), you may be underdriving the Henry. If your amp or repeater has N connectors, check the bifurcated center pins. I've had them spread out causing terrible connections, too.