the not being perpendicular thing might be a result of many things:
1) you missed to install the backplate properly (pic needed)
2) it's indeed deformed because of heavy abuse (Pic

)
3) it's likely a chinese copy, and although they tend to work just fine and are commonly reliable..
it's still a chinese copy and you might have gotten the one in a thousand that's poorly made (Pic again I'm afraid)
4) misaligned sprockets can cause many issues, normally premature failure of the chain and sprockets, sometimes failure of the jackshaft bearings... *shrugs* (A pic could help though)
We like to help you out, we really do, but as you said it's hard without "seeing the problem"
I've seen people bolting the backplate on with one single bolt (that WILL fail)
all four are required to have a sturdy backplate!, all four need to be torqued down in order to not losen the bolts while driving (loctite

)
etc.etc.
If we can see what's wrong, we can tell you what to take care of, what to fix.
For now, all explanation only can tell us so much about it... no matter how hard you try I'm afraid;
it's the two things you forgot to mention that might be key to finding a solution.
Yes, the backplate mounts to the engine, and thus should be perfectly perpendicular to the PTO shaft,
but only if you haven't messed up (forgotten bolt, a misplaced washer...)
Oh wait... waaaaaait..
you have the cast backplate don't you?
(the pressed sheet steel one is for mini bikes mostly and deforms rather easily under tough conditions like bad gear ratio or misaligned sprockets

)
Again a Pic would've helped LOL (okay enough, I think you got the point by now

)
Anyways, we're here, we'll figure it out and we can tell you how to fix your current issue as well as prevent it from happening again; but we need your arms, eyes and wallet to do so I'm afraid
'sid