I just installed MyAlerts 2.0.4 on my board and it's messed up on the Square theme on my board......
here's a pic attached....
board URL:
https://www.nucleusboards.net
try replacing li element with span element in myalerts_headericon template
That's fixed it, partially. :
Is it possible to put it after both the admin CP and Mod CP links?
This is how it looks now, it's kinda mashed between the two?
you can change that order in header_welcomeblock_member template
find {$myalerts_headericon} & move it to required place
[after {$admincplink}{$modcplink} - may be you have this in reverse order !]