some folders are missing in the Deploy folder (i.e. Applications, Captures, Out-of-Box Drivers, Packages, Templates). Could you please compare the content of the C:\Deploy folder with the content of the Content\Deploy folder of your MDT Bundle?
Apart from the folder “Operating Systems” (that is imported at upload time as OS resource, if present), you should find the same content.
If the folders are missing in the MDT bundle itself, probably it’s corrupted and must be recreated and re-uploaded, while if the folders are present in the MDT Bundle and they are missing only on the target computer in the C:\Deploy folder, maybe some problem occurred at uncompress time. The resourceUnzip.log file should be in the folder:
C:\Program Files (x86)\BigFix Enterprise\BES Client__BESData\actionsite__Download
(but it could have been deleted if other actions arrived to the computer).