After much research I figured out a solution. Strangely, even clocking externally didn’t help. I clocked from every conceivable source to every source to no avail. The source video was at 48kHz, so I have no idea where the 44.1 kept creeping in. Even stripping the audio completely from the QT file doesn’t work.
The solution lies in that QT doesn’t actually run inside N4, but rather concurrently. So both QT and Nuendo are jockeying for ASIO priority, which triggers a samplerate switch. The best/easiest solution was to enable the on board soundcard and assign Windows to use that as the default output. QT has the on-board sound card and Nuendo has ASIO priority. Simple and done. This appears to only be a problem with MOTU stuff. I had an M-Audio usb interface that I dropped in for testing and it worked fine no matter what.
But in the end we just upgraded to N5 to see if it would help, which it indeed has. 2 video projects since the upgrade and no glitches yet! Cheers!