It's been a while so I may be remembering incorrectly, but I always felt like they seemed to have hidden/unannounced time limits for getting the achievements completed if you wanted to get a pin/reward. For example, they probably had limited supplies of pins and so thewy seemed to send them out on a first-come/first-served basis (first-to-achieve/first-to-receive pin). You probably already know this, but getting an achievement didn't guarantee a pin or other mailed reward.
Were you pretty quick to get your 999 kill achievement (e.g., within hours or a day of the game launching)? Even so, if they had limited quantities, you might not have completed it before hundred(s)/thousand(s) of other people did. That's the only explanation I could think of? Or maybe your achievement was just accidentally missed by the Flynn Lives people
Sadly, at this point I'd say it's probably way too late to expect to get one from the ARG. I tried to contact the Flynn Lives people back in early 2010 for something, but no response/no swag was ever received in relation to my email.
The email address I used to try and reach them was "firstname.lastname@example.org", but I doubt it's still used. In an unrelated email I had received from them, it said this in their signature: "Flynn Lives is a volunteer-based organization; we respect our members' busy lives...etc." Surely the volunteers are no longer working on the ARG 2.5 years later? Just sayin', in case it helps.
PS: If anyone wants to play Space Paranoids, it's still available! This is NOT the one that the 999 kill achievement was from, though: http://www.spaceparanoidsonline.com/
And here's the one for the 999 kill achievement:
Just shoot the recognizers that float across the screen. It keeps track of your score in the upper-left. Granted, there's not really much point to racking up 999 kills since the ARG is over.
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