You have hit on a problem that is endemic in Linux at the moment, there are so many sound controllers and volume controls that it is very easy to make this mistake and the mistake is not necessarily yours, imho it lies with developers for making the whole thing overly complicated or perhaps failing to see that it needs simplifying.
If you count graphical, comand line and hardware modes, I recently found that there were 7 different ways to adjust the volume on my laptop, and not all of them work with each other, this is nonsense.
Fujitsu Lifebook AH532 Laptop. Intel i5 processor, 6Gb ram, Intel HD3000 graphics, Intel Audio/wifi. Realtek RTL8111/8168B Ethernet.Ubuntu12.10 (Unity), Mint14 (Cinnamon), Manjaro (Xfce).