I had the exact same situation. I installed a 32gb micro. I formatted it through Windows. This allowed it to be seen on my computer and even on the Clip+. I transferred my files to it. When I tried to access them the file showed empty. I then updated the firmware. No change. I then came to this forum. In reading the threads I found that you need to format the micro with a special formatter. I downloaded this formatter an re-formatted my 32 gb micro. It now works like a champ. I can copy my files and they show up just fine.
No special formatter should be needed. Having said that, the SD Association’s formatting tool sometimes can clear away problems and is a good source to try.