We have had several instances with Java updates where the client machines look like they are still installing the Java update, but when you go look Java has been updated. 50 minutes later if you do a restart on the machine it seems to take care of itself. Has happened with both r30 and r31 versions.
If by "...appear to still be installing..." you mean that the console is indicating a status of 'executing', this would suggest that there is something preventing status updates from being sent or recieved. The console machine does not actively monitor deployments. Rather, the target machines process deployments, and send periodic updates to the console via TCP3121.