If the LNBF works correctly if only one coax is connected at a time, I would rule out a LNBF defect and test for interaction between the two coax cables/STBs/AC power.
Are you using a multi-switch? Is the "0" skew marking stamp aligned with the dish polar axis (12 o'clock) or with 3/9 o'clock?
Are the two STBs located in different rooms or in the same room? If different rooms, test for power line interaction by running a temporary AC extension cord to power the STB, TV (and other connected AV devices).
Also, with the STBs connected as they are currently, check for potential voltages tested between the two coax cables (braid to braid, braid to center conductor and opposite braid to opposite center conductor) when disconnected from the LNBF and connected only to the STBs. Repeat the test with all AV devices connected.
Also note that sometimes tuners also will only interact when tuned on specific transponders and knock out a TP on the other STB.
Have noted many time over the years that multiple STBs located on different electrical sources can interact with multiple output LNBFs. Sometimes the can be identified to be the result of the home wiring, incorrect grounding, ground loops, voltage on neutral, a voltage detected between negative and ground, mismatch between tuners/STBs, etc.
Remedies include lifting grounds, installing a powered multiswitch, grounding/binding the dish to structure ground, etc.
Hope these ideas help you identify and slice the problem.