Step 1. Move your bot to other channel (not by botjoinchannel command)
Step 2. Type /botjoinchannel <previous channel id>
Step 3. ...
Step 4. Profit
<15:35:25> "superuser": !botjoinchannel 25451
<15:35:25> "superbot": Bot is already in the given channel!
Thanks for reporting. I already have an idea why this happens, but it has no priority. It will be fixed in one of the next versions.
It's now fixed with JTS3ServerMod 6.2.0, was released some minutes ago.
Thanks! Can confirm that this is now fixed.