I am running VarAC 12.0.0 in two instances. One with an Icom 7300 and the other with a Yaesu FTDX10. Each instance has it's own ini file as required per the user manual.
OS = Windows 10
VarAC is running in cluster mode. the 7300 instance is node 1. The FTDX10 instance is node 2.
In the example screenshot, the 7300 is on 14.105 and the FTDX10 is on 7.105.

Normal behavior
The 7300 is writing beacons and CQ calls to the database with the instance_id = 1.
The FTDX10 is writing beacons and CQ calls to the database with the instance_id = 2.
PROBLEM: Some beacons are written to the database twice. Once with id = 1 and the other with id = 2.

The table is sorted by id descending. The latest entries are on top. Look at the top 6 entries. These are really 3 entries duplicated.
It looks like duplicates are created whenever the locator data is present. In other words, any time you see a locator populated in the database, there is a duplicate entry (when running in cluster mode).
Check your port settings with the modems... seems like both VarAC instances are capturing KISS data from the same VARA modem.
the input about only with locator and broadcasts indicates it is a KISS traffic and not standard (As advanced beacons and broadcasts are using the modem KISS interface.
As the time stamps are not identical - it is clearly 2 difference VarAC writing the same data. There is no data sharing between the instances so the only explanation is that they are getting the same traffic someone from the same modem , possible through a PORT splitter allowing them to listen to the same port.
Bottom line - please check your port numbers on the modems.