I had this same problem at lunch today. I earned the alternate syringe gun the night before and used it in game. However at lunch, it said it was equipped, but it wasn't and I couldn't get it back. What worked for me was: Equip the plain syringe gun while in game, quite the game, quit Steam, relaunch steam, enter a game and then select the alternate. After that, I was able to use the new gun again (which i am liking. It has saved me a few times already =)
-Groo