Look in your settings menu at the USB mode...from what you're describing, I suspect it is on "Auto-Detect". If that is the case, do the clip+ internal format to clear everything out....then you need to choose either MSC or MTP and stick to one or the other. Since you are in the habit of using Explorer already, sounds like MSC would be the way to go for you.
iPod Touch 5G 32GB, Touch 4G 32GB, Clip Sport 8GB. Rockbox-> Clip Zip 4GB, iPod Nano 2G 4GB, iPod 5.5G 80GB
2012 Nexus 7 32GB, Asus MeMoPad 8 16+64GB, LG Optimus G Pro, Nokia Lumia 900 and Lumia 520