A friend of mine and I just finished a 2-player Eikthyr run we were planning to submit, but we both recorded using NVIDIA Shadow Play, which appears to automatically stop recording during some loading screens (in particular, when connecting to the server prior to the start of the run).

For example, in my video of the run you can hear the audio skip at 2:14 and 2:19:

Would this run (and similar) still be considered valid, or should use of Shadow Play be disallowed for this reason?

I'll allow it.