I am also seeing this. I have tried a few things such as deselecting/res-electing gem types, adjusting quality of gem to pickup, and clicking to pick up items of all types. None of these efforts were able to force gem pickup.
It seems my anti-virus was preventing updates. After I resolved this and updated from 487 -> 489... Gems! Thanks for the help. It also seems to have help with potion storage/sorting as well.