After some more investigation i found that when a large log backup was required to be taken, the time taken produce the trn backup file was elapsing a timeout period of 5 minutes set by the lanmanserver service.
The error being reported was error 64 (error not found) which is actually quite a common issue apparently as described here; so even though the log backup was being created, the SQL engine couldn't verify that the backup had been successful.
In turn, the VLF's where not being set to 0, hench seeing the issues that were described in the Question.
thank you for your help guys, but i think the root of the issue was the error being reported (i didn't mention that as i could see the backup files and logshipping was still processing them, so i didn't think it was part of the same problem!)
