Haven't come across upside down photographs before, but videos certainly have that habit.
I suggest you consider the orientation of the iPad when taking the photograph. Home button down for portrait, and to your right for landscape.
that sorts out video. It may be the same for photos too.
Try a different USB port, preferably USB2.0, and do not connect through a USB hub, not even a powered one.
Once the PC has found your iPad, you right click on the iPad icon in Windows Explorer, and select Import Photographs from the popup list. There is an option to delete the photographs after transfer. It works OK, and is the fastest and most reliable method for deleting large quantities of photographs from the iPad. Don't delete them by deleting from the DCIM folder. That has caused major issues in the past.