I have 10.11.3 on both effected Macs. There are several card readers and brands of cards all returning the same issue - I tried swapping them around before I posted on here. For the record, the card readers are Lexar USB3 Dual Slot, Pixelflash No bend Pin CF reader and a Delkin USB3 SD & CF reader. The cards are both CF and SD and all but one of them are Sandisk and the odd one is an Eye-fi card. It also happens with the computer's own SD slot.
The only other thought is that I have used the Terminal command { defaults -currentHost write com.apple.ImageCapture disableHotPlug -bool YES } to stop Photos opening every time I put a card in (which works by the way).
Otherwise, I am totally foxed too.