Might not be ST2's fault, could be borked line-endings.
Did you get this file from a machine running on a different operating system? Like perhaps your webserver via FTP?
We had a developer at my last place who was using some weirdo-FTP client and it kept trying to 'fix' line endings when going from a Windows box up to the linux server. Resulted in the same as what you have.
I'm sure there's a plugin that will remove blank lines (Notepad++ has one) but it won't fix the cause of the problem if I'm right.