Sorry,I'm not sure why the cookies weren't recovered from quarantine.
Your good cookies are probably being cleared if you have usage tracks checked for the system scan.
http://www.safer-networking.org/faq/usage-tracks/
It's different in Spybot 2.4,tracks are no longer shown as green.
If you'd like to continue scanning for usage tracks,you can look through the list,and uncheck the cookies for Sea Monkey before you hit fix selected from now on.The Sea Monkey cookies will be listed under cookie,and will say Mozilla beside them.
Or,you could stop scanning for usage tracks altogether,just open Spybot start center,Checkmark advanced user mode,click Settings(say yes to the UAC prompt),then the Categories tab,and somewhere within the window,rightclick and select Spyware Scan Only.