Yup, that'll explain it. Your show's 23.96 framerate is the equivalent of 24hz; so dropping your desktop to that refresh rate should alleviate the issue.
Of course you should be able to just disable the refresh-rate-adjustment within the video player as well.
Any changes to refresh rate on a single-chip DLP projector will require a re-sync of the color wheel: your older projector would've also blanked for a little bit; but if it had a slower color wheel (which was probably the case), it might've been able to sync faster.
But as for the 5 seconds or so it's taking you when display refresh rate changes: with a recent DLP, that's normal. I have roughly the same delay with my W1070.
BenQ W1070 Projector; Xtreamer Ultra 2 (running XBMC on OpenELEC) via Sony STR-DH540 AVR with Boston Acoustics SoundWare XS SE 5.1 Audio. MediaBrowser3 for Mobile Streaming.
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