Does it happen with only one connected? Or only when both are?
Lets figure out the trigger, then maybe we can find a solution.
I can think of:
Only 1 of the 2 docks triggers it
requires both to trigger this.
A second Monitor triggers this, either dock.
I am assuming your Mac only has one Thunderbolt bus (two ports)
So there is no way to keep the two docks on separate buses.
Are the extra dock ports for Thunderbolt enclosures? Monitors? or USB devices?