I've given it lots and lots of time to try and work with it, and I wish I could come to the same conclusion as you did, "easily resolved"...
I've ended up disabling the seamless feature, no matter how much I wish to use it, it's just far too much hassle, going purely with hotkeys now.
I hope you get around to fixing this, I'd really like to use the seamless feature in conjunction with hotkeys. The way it is now that only works for me without using modifier keys on the hotkeys.
Or if this is something you can't reliably reproduce, let me know if I can be of any further assistance, unfortunately my regular use scenario is capable of reproducing the issue 100% of the time.
The seamless feature was one of the features I wanted when I bought Multiplicity, so I don't mind putting in some extra effort to try and solve the issue.