They count as jumps as in your total number of jumps in general. I think as long as you complete the requirements of the "A License" You should be able to count the jumps if you needed extra towards the total number of jumps for your license, just for numbers sake.
When I went to HALO we did two night jumps, and I plan on using them for my D License. Just because it's military doesn't mean it doesn't count. You just need to fulfill the requirements of the license, per se.
Have fun at skydive paraclete. I'm assuming that is where you are at. You got an awesome drop zone for just getting into the sport.