Card reader disappears

After installing El Capitan the internal card reader will disappear and post the following notification "Disk Not Ejected Properly etc."

By disappear I mean it is no longer reported in System Report, Hardware Overview and no sd card is recognized. This continues until after a restart when all appears normal showing the presence of the card reader. When a card is inserted it will mount. I can eject and insert several times and all is well. After some time, minutes to hours the mounted card disappears and the "Disk Not Properly Ejected" notification appears. A restart is then required to get it working again.

System report - Hardware overview will show the card reader present until it stops working. Then it shows "This computer doesn't contain any Apple internal card readers".

I have read through older posts about the switch inside the card reader and resetting SMC and PRAM none of which has any effect. It works until the Eject notification but the simple restart is the only thing that temporarily gets it to work. I have replaced the card reader with a new one. No help.

Trying to isolate the problem, I boot from a Yosemite clone and find the card reader is solid. Ran the iMac that way for several days with no problem.

Not running any VM software or any apps that could be blamed (that I know of).