First you shouldn't short the D+/- lines to ground. The Dedicated Charging Port spec is D+/- shorted, and no connection to 5V or Gnd (at least in the documents I've found).
I hate to state the obvious, but it has to be asked: are you sure you got the pinout right? You didn't accidentally switch 5V and Gnd, or connect your data lines to 5V, did you? If your PC doesn't recognize your phone at all, it does sound like you damaged the USB circuitry on the phone.
The note about an app being uninstalled is probably entirely coincidence. Though, for peace of mind, I'd try restoring a nandroid backup (you do make those regularly, right?) from a few days ago and see what happens with your computer.
In my experience, phones will say they're charging if they see 5V on the USB port. The charge IC may have died, so it won't charge the battery, but the rest of the system still sees the 5V there. I'm not sure what kind of charge controller they're using, but it might be of the kind that directly interfaces with the USB data lines for charger type sensing. These usually connect straight to the USB port, and when they've detected what kind of charger you've plugged in, they turn the USB data lines over to the main processor.
If you've killed that chip, maybe by connecting D+/- to 5V (or more), it won't switch data over to the processor, so your computer can't see it anymore.