ok I tried again and this time there is no doubt at all. the count is reset.
I took a mission for 3 pirate kills.
I go to the NAV and kill 2 pirates. confirm the kill count is 2
I go find a USS, and sure enough get alternate mission of massacring cops. kill count disappears.
Back to NAV. kill one pirate. kill count is 1
kill 2 more, mission completed.
I caj confirm at my end isnt bugged.
We must have different clients.
I get mission to kill 3. Kill 2 shows two killed. 3 target.
Get alternate offer. Mussion description goes to kill 3 target. Alternatively abandon.
NO LONGER DISPLAYS ACHIEVED KILLS.
Kill 1 more pirate mission completes.
I think you guys are confused with what pirates are (as is evident from a lot of posts) and kill 2 bounties and a pirate and think it reset. It doesnt.
Ps Another way to spot pirates is the ship paint job so do a flyby if in doubt. Skulls = shoot.