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Have you changed any settings regarding USB connection?
You must have an app installed that when connected to a USB device like a Pc it is set to dismount the SD card and mount it as an SD card on your Pc - I remember Winamp did this
Well if you've installed nothing then perform a system repair
Performing a system repair using Pc Companion will factory reset your phone
Switch off your phone and unplug from Pc (Hold volume up and power for around 10 seconds)
Start PC Companion and select Support zone then Update my phone/tablet then in Blue Repair my phone/tablet and follow the onscreen instructions - When prompted connect your phone still switched off holding volume down or back button - This should start the repair or reformat process
If you are using Windows 8/8.1 or a 64bit operating system then adjust the settings for PC Companion and run in compatibility mode and chose Windows 7 or XP
Yes but you said it was like stock so nothing lost
Back them up