I have 3 gateways with the 2.5.0 version of the LoraServer all 3 gateways were seen with Gateway discovery, updating to the 2.6.0 version are seen only in pairs.
There wasn’t any change to the gateway discovery in the update (also most of the gateway discovery is implemented in LoRa App Server, not LoRa Server). If you think this is a bug, please create an issue (https://github.com/brocaar/loraserver/issues) with all the details needed to reproduce this.