No, i use my phone as an alarm sometime as well and there is nothing wrong with doing that. What I am implying is that sometimes when we hack and mod our devices and load with 3rd party software, other minute side effects can occur. If you think AS is causing the issue then close it out by (in XP) going to your task manager and closing wcescomm.exe and leaving it in the cradle. Another way would be to not leave it connected to the PC but rather to a wall charger. If your phone no longer has those same issues with you still using it in the same manner then you know what your issues is/was.
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Loving my rooted Droid X
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