Fuel not draining correctly after undocking

[Guy the Wise]

Hi; I'm having issues with my fuel not being used properly after undocking from another craft.

So I have this early quad-engine interplanetary tug ("Steamboat Willie") that's designed to ferry crafts, fuel, and other stuff between low Kerbin orbit & Munar orbit, with one central tank (FL-T400) under the probe core and 4 engine/tank setups (T100, T200, Terrier in that order) placed around it radially. Plenty of solar panels, batteries, and RCS. Launched it as a probe type and flew it successfully until now.
After dropping off some fuel in Munar orbit, I ran it back and picked up a couple rovers and a 'delivery system' for the Mun; the plan was and still is to use the lander (delivery system) to drop the two rovers onto the Mun's surface and then put together my first base. First, however, I docked it to a temporary fuel depot in LKO and used an orbital tug to move the rovers near Steamboat Willie; had to undock the rovers first and then catch them to put them on Willie's left & right. I then added the delivery lander to the aft, fueled up everything, and tried to take off, only noticing the problem when trying to do the transfer burn.
Testing in the VAB revealed no balancing problems, so I eventually had the bright idea of checking fuel consumption. Sure enough, both the 100 & 200 from one of Willie's corners were draining faster than the others. As well, that engine was showing up as empty in the staging, despite having plenty of fuel and firing correctly. However, for some reason, I can remediate this by setting priority so that the affected tanks and their opposites drain before the other 5 tanks.

I'm not sure what's going on; did docking with so many crafts at the fuel depot cause some sort of glitch? Read from a posting about 10 years back that the fuel system was easily confused.