As Captain Widebody has said, it is important that each relevant page is certified. Also, that Section 2 (Special Flying Qualifications and Renewals) and Section 3 (Instrument Ratings) clearly include your name.
Some of the CAA licence production team are quite new to the game and may not understand the full range of military terminology. When I applied for my ATPL in 2002, I had a call querying that Section 2 of my logbook didn't include the words 'Combat Ready'. I pointed out that CR(S) was a higher qualification; however, no-one had actually briefed the CAA about the system, so I had to fax them the relevant extracts from GASOs as proof.
Hardest part of the whole process was filling out the 'Flying Experience in Military Aircraft' section of the form - how I wished I hadn't bothered to log those few trips in the Dominie, Beaver and Meteor T7 in the 1970s!