It's a 6.03 glitch unfortunately. Not from pirated software.
I'm having a similar issue and I have the creative cloud.
There's not much documentation on it online but I found some other people having the same issues elsewhere.
What's happening for me is premiere stopped recognizing the audio track on a particular mts file. It started after the 6.03 update.
The file was and is fine, it loads perfectly on cs5.5 on a different machine.
The solution they found which worked for me as well was downgrading to 6.0 via reinstall.
Hopefully they'll sort it out in the next update, because my video card appreciates the 6.03 upgrade in a big way.