Unfortunately the latest release of AIR2.6 in the Flex 4.5 SDK, (bundled with Flash Builder 4.5), has presented a familiar problem trying to auto-update your applications from AIR2.5.
http://forums.adobe.com/message/3650502
We’ve seen this issue before trying to update desktop apps from AIR1.0+ to 2.5 and had to follow a hacky workaround to get users working with the latest version:
http://kb2.adobe.com/cps/873/cpsid_87300.html




