In the past I sometimes had these issues with my clients’ QuickTime-videos which had heavy compression on a particular frame or on a particular sequence.
Nowadays I usually convert all my clients’ videos to a DNxHD 36 Mbit/sec and that solved the issues.
At least: when I use conversion from “DNxER” by ER Media Toolkit, the issues sometimes re-appear, but when I use conversion from “MPEG Streamclip”, I have no issues at all… I don’t know why.
In order to play DNxHD videos properly in Nuendo you have to (buy and) install the DNxHD Decoder from Steinberg.
I don’t know if this solves your issues, but maybe you can “investigate” the type of compression of your clients’ video and the load on your CPU during this particular frame or sequence? From the load on your CPU you can at least tell what is happening in your computer during the video…