Also, check your inventory, you won't pick up if your full, or it will put you over weight :)

try checking the keybinding for the auto pickup enable/disable. Since it was added in the patch the default key might conflict with another keybinding you set up if you made changes to the defaults.

Its on the settings menu, controls, bottom of left colum.

I had to change the keybinding for it right after the patch as it conflicted with the custom keybinds I had set up and I don't remember the default key for it but I do remember it was in the cluster around AWSD like all the other default keybinds..

try without mods... it works fine for me, I pick up until 1) full or 2) overweight.