Switching to the MasterCraft Green Impellers
will decrease your fill and drain times which might be the easiest fix to the problem. They are stiffer than the yellow impellers and will also hold the water back if you are experiencing a passive drain issue.
I think the pumps are turning off because they are running out of time. You have a 2007 with the 6 minute max factory timer modules. Most of our customers opt for the MasterCraft Jabsco 20 minute Timer Modules
although some do rewire the system to eliminate the timers. You do get a fair amount of water in that short time period but it is draining slower than it is filling so the pumps are shutting them selves off. I might be wrong and you might have already changed out the timers.