This is a small bug that has been around for a while, but I don't think that anyone has reported it..
If I try to re-arrange the order of my protocol accounts (under 'Options' > 'Contact list' > 'Accounts'), my first attempt always seems to cause one of my accounts to disappear from the status bar, after clicking on 'Apply'.
..but when I mess around with it a bit more, it re-appears and everything seems to be OK.
I'm using the classic contact list btw.
(Miranda NG v0.95.5 (x64) / Windows 8.1 Pro (x64))