Actually, I have a different problem. When I connect my Kindle2 to my laptop and leave it there for any length of time it seems to mess up my Kindle's charging memory.
Not only does my Kindle seem to run out of juice fairly quickly, but it also runs out quickly on the next charging cycle. Or so it seems. I've never actually run it dry -- I'm just going by the battery meter.
I have assumed that the problem is with the USB ports on my Dell laptop. Dell has been known in the past to have underpowered USB ports that don't do a great job with charging devices. I further assume that the Kindle thinks its getting charged because it recognizes the connection, but it is either not getting enough juice, or even drawing current to stay awake. The bottom line is that it takes a couple of charge cycles to get back to normal behavior.
On the other hand, the issue for you is that I wouldn't be sure that cutting the USB charging circuit would give the results you want. Your Kindle might really be confused if it thinks its hooked up, but it isn't getting the juice it thinks it should be getting.
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