I experienced an issue on a laptop recently, which has the PDQ agent installed. Microsoft's Monthly rollups had been failing to install each month for around 4 months and I finally wanted to resolve this.
I posted logs to Sysnative and someone suggested uninstalling the PDQ agent and retrying. The Microsoft update then installed first time. The 4 months of failed updates tallies with the time I rolled out the agent.
See following articles
All issues were resolved by temporarily uninstalling the PDQ agent.
I just want to check whether PDQ are aware of this, as the latest reply in the 1st link suggests Sysnative have already contacted you about this.