Location List locations contain the line number in them about syntastic

[blueyed]

Try it with increased ":verbose", so any autocommands that might change the buffer get displayed. I would start with ":verbose 9".

Also, I had seen a snippet to prepend line numbers recently, you might have installed something in that respect. See e.g. http://vim.wikia.com/wiki/Insert_line_numbers

[brandonw]

I figured out the problem: it was the errorformat. I am readying a patch to fix.

Thanks,
Brandon