Your CSS for the treemenu and the code for the treemenu appear to be out of sync. My guess would be that your non-indextreemenu.php implementation has some of the same div names that are conflicting with another newer css file.
I found the problem. It was in ezjaxx extension which is not compatible with eZ 3.10.1. I think I'll remove ezjaxx since the only big advantage I got form it is the dynamic contentstructure menu which is dynamic in ez 3.10.1 by default.
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