This same issue is now an issue for me in visual studio 2012 - that sometimes if I use the debugger; command within a js file, the latest version of the js file is NOT shown, a previous version is shown instead even though I have my IE cache settings set
correctly etc.
http://social.technet.microsoft.com/Forums/en-US/sharepointdevelopmentprevious/thread/359ee3ee-0fc9-454e-b9fb-e9a4f81cb87f?referrer=http://social.technet.microsoft.com/Forums/en-US/sharepointdevelopmentprevious/thread/359ee3ee-0fc9-454e-b9fb-e9a4f81cb87f?referrer=http://social.technet.microsoft.com/Forums/en-US/sharepointdevelopmentprevious/thread/359ee3ee-0fc9-454e-b9fb-e9a4f81cb87f
PLEASE NOTE I am only putting this question in this forum because that is where the previous thread was (I recognize it was in the wrong place)