It almost sounds like you have the AUX port enabled for data, in addition to sync, creating a network loop. Ensure that the AUX port settings under the Configuration>IP tab are not enabled (Power and Data). However you would want to enable the following settings:
Radio #1 BHM Sync:
General > Config > Sync Source > Generate Sync
General > Config > Sync Output > Aux Port: Enabled
Radio #2 Receiving sync from BHM via AUX port:
General > Config > Sync Source > AutoSync or AutoSync + Free Run
General > Config > AP Type: Remote AP (not strictly required, but recommended)
The cables should all be standard patch cables connecting to the network equipment. The cable connecting the AUX ports together will need a custom pinout. See this post for the pinout (you only need the AUX port pins, blue and brown, since you are only passing sync and not power).
The easiest fix is to connect a uGPS/cnPulse to the two BHM's and configure them both for AutoSync + Free Run, but I think you are sending over more than just sync between the two AUX ports.