OS?
Have you tried to go back to last known "good" version?
Last Known Good is overwritten once the computer makes it to the desktop.
Maybe a system restore to a point before you noticed this issue.
Is it all USB ports that do not recognize drives?
Have you tried the ones in the back of the machine that are directly connected to the Mobo?
I mean it is kind of strange that both of these issues would occur at the same time, This kind of points to either mobo failure. Or as cadaver had pointed out a Operating System issue. (Software)