We had issues with the PXE Service Point Point the day before and had to reinstall PXE service Then upload all the now missing packages It turns out the SCCM agent package didn't update correctly on the distribution point.
'Refreshing' the package fixed the issue. Don't just 'Update' the DP as this just does a compare and uploads if different. Refresh copies all the files again.
If you are having this problem yourself i'd like to hear from you about it. Please leave a comment I might be able to help.