I just wanted to close off this thread and thank all for their suggestions and support.

I think the issue was down to the print drivers and the print server, not pcounter as I initially thought, it appears that in beefing up the VM spec a bit in anticipation of the demand with isolation and turning on Driver Isolation on the print queue on the server, I have cured this problem, I have not had a job reported to me as disappearing within the last two weeks that its been active now. *touches wood*

I have isolation on for our MFDs now that people can print directly too as a further precaution, all is well so far.