After basically removing all possible chunks of code from our implementation - it turned out that we had a (stupid) wrapper class that wraps MFCLeakReport class.

In it, there were calls to _CrtSetReportHook. Removing these calls completely solved the issue. As for why this was there for my company, or how to implement it correctly is irrelevant for the solution - but if anyone ever encounters similar behavior - try looking for MFC hooks.