That makes sense. The iControlPortal is implemented as a single FIFO queue to avoid two callers from stomping on eachother. If there is a process (in your situation ConfigSync) that is communicating between the boxes for a long lived connection, then if you are trying to make an iControl call to the same target box as your BIG-IP is, you'll have to wait for the first call to return before yours can be processed. I'm surprised that this is taking longer than your intervals. The only other issue I could see is that a load of the configuration forces a restart of httpd which will cause iControl connections currently in the queue to be aborted.
I'm going to have to get my head around a viable solution to this issue...
-Joe
Nimbostratus