Melchett
It's not clear from your post - has funding approval been given for the course or were you expected to (a) attend or book the course and seek retrospective funding approval [perhaps because the requirement to attend the course is short notice] or (b) ensure funding approval was in place prior to attending.
If (a) then I would agree with your sentiment that it sucks (although if it is an op-related course then (if memory serves me right) your budget manager won't give two hoots as he will be able to claim back the 'overspend' against the (so called) op budget). If (b) then the JPA advance is there for just that reason. Quote either of the staff officers as your authority (having got them to confirm the requirement via e-mail) and hit submit!
Of course, being a NATO course it will be stretched out at least as twice as necessary!