Ok, so it looks like the paperwhite has the same usb ids as the Kindle 2/3/Touch. That makes it even odder that it seems to work differently than those devices. Can you do the following tests:
0) delete the files you recently sent to the device
1) Right click the kindle icon on the calibre toolbar and select configure this device. Uncheck the option to use sub directories. calibre should then put files directly into the documents folder. See if sending a mobi like that works.
2) Again configure the driver, this time telling it to send the azw3 format instead of mobi. Check if the azw3 file works (both in subdirectories and not in sub directories)
Also are you generating old style mobi or the new "combined" mobi that contains both kf8 and mobi7?