That might be a bike-specific observation, Mike....at what RPM are you shifting? FJRs are notoriously bad when shifted at low RPMs. Even my XS1100 would shift decently at 2,000 rpms but my FJR is much happier over 3500 rpms. When it was newer 4k was it's happy place.
If you are "short shifting" (at 2000 rpms, for instance) that might cause the issue you are describing.
My 2005 shifted noticeably smoother at lower RPM, say around 2000, than it did up higher. Then again, the difference could have been that I rarely used the clutch for upshifts, I don't know.
To the OP, I would suggest finding a riding partner and swap bikes for a longer ride than what the Service Manager did. This is just to rule out any unusual shifting technique that you might be unintentionally using.