The only way I should see this happen would be either of 2 ways
//echo -a $mircini
if this is located in a folder where you don't have write permissions, all disk writes to it would fail, and the client would start every time using an unchanging mirc.ini
Another way would be if something causes mirc.ini to be corrupted as mirc writes to disk during exit, causing the client to reset mirc.ini from scratch. You can't tell from $file($mircini).ctime because of the way mirc updates files, causing the 'creation' time to always be updated
Either of these problems wouldn't affect your alt+D aliases file, because those are in a separate aliases.ini, and the default mirc.ini contains a reference to it. If mirc.ini is being reset from scratch, it does clear out all the scripts in the remotes tab of the alt+R editor