I just upgraded to the latest versions of Multi-Domain and Domain Mapping and I am pleased to report that it didn't crash my sites (the last time I upgraded both it did crash).
Many of the bugs that I previously reported have been worked out (all the major ones). However, there is one that is still aggravating me. I am sure it is still on the board for being addressed but I just wanted to remind you.
I am using WP 3.1.3 on my primary site with many plugins and Multi-Site and Domain Mapping. (I know, I know upgrade but I hate all the headaches that it always creates - maybe next month).
Anyway, Site Search for Multi-Domain sites does not work.
To confirm whether this relates to Multi-Domain or WP or one of my other plugins I took the following steps.
Fresh install of WP 3.3.1 with Multi-Domain installed on it's own. Added an additional domain. Added new site on second domain. Search for site using the full sub-domain or full sub-domain+domain, and nothing returned in either case.
So, my conclusion is that Site Search with Multi-Domain is broken. If this can be resolved it would be great because it creates a serious difficulty in searching for a specific site given we have 300+ to look through.