Interesting. As I mentioned I still run WP Super Edit on a number of websites for the university I work for. These sites are both standard WordPress and WordPress multisite. My guess is that you have a plugin that is incorrectly filtering the tiny_mce_before_init filter.
WP Super Edit passes all TinyMCE settings through that filter. If WP Super Edit appears to be working and you can drag buttons, activate TinyMCE plugins properly, then the filter is a likely culprit. I’ve seen it happen many times where theme and plugin authors use that filter, add their special button, but don’t allow any other plugin to pass data through the filter. It’s impossible to work around and must be fixed in the other plugin.
Typically if this mess called WP Super Edit fails, it fails in a catastrophic way with annoying errors and completely broken editors. If you find out any other information that I might be able to replicate on the systems I maintain, let me know. Please note that I have not tested yet with WordPress trunk and I would not be surprised with issues there since the core developers are actively working to upgrade TinyMCE to 4.0.