Not clear your problem for me.

I think the warnings comes templates conflict in database. XOOPS templates administration little bit buggy, some timings make miss consistency.

How to fix ... Well, I don't know silver bullet.
Try GIJOE's admin (altsys or tplsadm) module. Download here. Or fixed system table manipulate via SQL (e.g. phpmyadmin).
--
安冨 伸浩 (マイサイト管理人)