In my further troubleshooting, I've found that eclipse is a total dick.
This bug was the cause
https://bugs.eclipse.org/bugs/show_bug.cgi?id=304774
Apparently it has C makefiles for compiling and Ant builds for deploying??? Basically make targets by default call make on the build command you specify.
If you want to write a custom target you need to make a makefile.init file in the working directory.
Alternatively, if you used the xml code and put it in your build.xml like me, you need to specify in the make target to run the build command
ant -f ${ProjDirPath}/build.xml YourTargetHere