After server restart the clan tag is displaying twice in chat. Performing a reload of the BetterChat plugin resolves the issue... until the next restart.

We recently switched from the RustIOClans plugin to the one simply named Clans and this wasn't an issue with the other plugin.

Any ideas?

This plugin doesn't provide any clan tags, the other plugins you are using would be. If you are using Clan Tags and Clans, you only need Clans.