I found what my problem was. It was a combination of my bash script not handling spaces in my directory names and me not using the shell:true object corectly in the build system. So what works now is:
{
"shell":true,
"cmd":["check.sh $file_path && make PROJECTNAME+=$file_base_name install"]
}
It seems that with the shell:true object I don't need every input in the cmd list to be in quotes, just one long string.
(thanks to u/Scoo_ from reddit for suggesting the fix) Hope this helps some one else out
EDIT (17-3-2014): I have uploaded the files that I use for building my AVR projects to my git hub: https://github.com/Jesse-Millwood/AVR-Stuffs.git