This often happens on tandems, especially older ones, when the RD doesn't have enough chain wrap capacity to accommodate the wide gear ranges. In your case, the switch from the 12T to 11T small cog may be partially responsible, but also the chain is probably a bit too long. If its a double chainring, then even more likely the chain is too long.

Did you happen to notice if you did or did not have this issue before the swap?

And, even though you probably shouldn't ride in this cross chain gear, when you pedal in this configuration (when the chain is under tension) the chain is lifted up off the chainstay... you're not "chain sawing" through your frame while you ride.

Consider taking it back to your LBS and ask them, I guessing they would address the problem without charge. .