Last night I had a problem with my permalinks and page templates which after a lengthy investigation I found out was related to the fact I had a custom taxonomy "year".
Now I have run into another problem as documented by previous users here:
I also had a custom taxonomy "type" which I have now had to change.
Is there any documentation about what terms are an aren't able to be use as custom taxonomies? It would be good if some such documentation existed.
So for a start don't use "year" or "type" as custom taxonomies.
Perhaps this and other problematic items could be added to documentation here or somewhere similar http://codex.wordpress.org/Taxonomies