So on a PVE server I have a raidable bases, I can either give them ruleset "default" or the custom one i made "raid" to allow the bases to be raidable. For some reason, and this happened for quite a while, it was the reason I stopped doing them, But ive made a few more raidable bases and they worked fine for a few wipes, and then all of a sudden there is nothing I can do to make the base take damage, its like it just stopped reading it as that zone.. Very strange, anyone else have this?

I'd say double check the zone ID, lately, I've not been able to get the zone name to work with TruePvE. I've had to use the zone ID. So that might be something worth trying.

The most recent versions should allow name or ID.  Be sure to upgrade both TruePVE and ZoneManager.