I had a similar issue, running the same pump but a different Aeromotive regulator.
The thing with running from both tanks at the same time, is that your pump will always pull harder on the shortest side. meaning if a fuel line is longer one side than the other, it will always drain the shorter side more.
Im running my two pickups to a tee with two ballvalves.
The valves can also help troubleshoot if you have a line sucking air or a pickup.
Also something i had. One of my pickup tubes were cracked. It would do exactly the same thing you are talking about.
could be a tube, line, or fitting. After i got the pickup fixed. I still had some issues. Mine finally resolved itself when i got rid of the seperator, and ran the lines to a Tee with shutoff valves. (something i recommend anyways.)
My pickup tube was cracked at the top where the AN line screwed in. Ill find a picture shortly