Raise the Prepare Using Buffer under Preferences > MIDI > Playback and Recording to 500ms if it's at the new default (since X1) of 250ms. If it's already there, try increasing it in increments of 50 or 100ms until the problem goes away.
The difference between the two projects may be tempo. Tempo and note placement can interact with the buffer size in a way that makes it necessary to raise the buffer even higher. I had one project that needed 550ms until I changed the tempo by .5 BPM. And sometimes just moving a single dropped note a tick or two will fix it.
250 is problematic for a lot of projects on a lot of systems regardless of tempo, and processing power does not seem to be a factor.