I believe the problem was due to the imports being performed at "busy" times of the day. I performed one this morning, and noticed 2 machines missing. After refreshing my AD view, I noticed the machines were now missing from that OU - a collegue had moved them.
However, I do believe that there was something wrong, I couldn't see it in the logs, but there were messages like this:
"Deadlock encountered during MessagingResource.Save"
And the details do mention a computer name that probably was not imported. I cannot confirm this as all machines have now imported correctly.