I've been running SVN 1286 for a while, and recently moved to 1518. After I switched, I noticed that alts would only be updated correctly if I manually clicked the update button in the configuration screen, and whenever the profiler data was uploaded, alt data would always get wiped out.
It looks like what's happening is the rules are not actually being stored in the $data variable when they are read in during the MemberList guild_pre function call, even though it looks like it should. I was able to fix the problem by creating a global variable which I copied $data into at the end of guild_pre, then I copy the global variable back into $data at the start of every other function in the MemberList update_hook.php file (if you'd like, I can post a diff of my changes when I get home from work tonight).
I think this is the same problem that I described in this thread a while back. Essentially, when you iterate through each of the addons using foreach in PHP (at least in PHP 4.4.1, which is what I'm running), PHP makes a copy of each object in the array, so when you are reading in the rules and storing them, they're getting stored in the copy of the addon object rather than the original. I had suggested making an alteration in update.lib.php to work around this issue since I think the problem is in the use of foreach rather than anything in memberlist itself.
Hope this helps. It's my only complaint about an otherwise absolutely amazing tool, and if this issue can be fixed, you would absolutely make my year. Thanks!