Some more information regarding this problem. I hadn't tied considered the fact that I had recently changed computers (now Win 7) and upgraded to ACE 2013 at the same time.
What I tried on the weekend was to move the project from the NAS device I use as a server in the office and have them on the local drive. When I did this all the problems regarding datatbase updates went away. Not sure what causes this but it gives me a new path to follow.
Anyone else had similar issues with networked storage? I am curioius as to why it only seemed to affect the database as the drawings were all updated correctly.