Remove the application from your device and see how your application is installed to make sure that Flash actually installs the new binary. (mine sometimes doesn't).
Try disconnecting the phone, updating the device list, then reconnecting it and updating the device list before starting debugging.
Try the menu "Debug"> "Debug"> "On the device via USB"> select your device. (For this, the .fla file must be the active file in Flash.) Note: I am using Flash Pro CC 2014, although not CS6.
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