mIRC could easily fail in looking for current notice line in the window because a script echoed a line between the two fast notice, possibly a line that has the format of a mIRC's notice.
The scripting language was created for this, use it.
Regardless, I think most people annoyed by the linesep, myself included, have linesep = $null in options.

Looking for a good help channel about mIRC? Check #mircscripting @ irc.swiftirc.net