Not exactly sure what caused this error, because I've just now started testing everything, so all I can provide is this error that very recently appeared in my error logs:
L 03/05/2013 - 13:27:57: [SM] Native "Call_StartFunction" reported: Plugin handle 590059 is invalid (error 3)
L 03/05/2013 - 13:27:57: [SM] Displaying call stack trace for plugin "store/store-core.smx":
L 03/05/2013 - 13:27:57: [SM]  Line 338, C:\Users\Alon\Documents\GitHub\store\scripting\store-core.sp::MainMenuSelectHandle()
For reference, it's about 13:41 (1:41PM) right now, so that error occurred less than 20 minutes ago. I'm not sure if it happened when I started the server up, or if it occurred later though...