M.C.
Sorry if this seems obvious... when you wash the cup, do you pull the plastic stopper out of the top? Water can get trapped in there.
My parents had a cup at there house that was 'clogged', and when I pulled the plastic piece out of the top, it was 'clogged' with thick black gook! GROSS!!! They had no idea that the plastic piece could come out. They had just kept washing it in dishwasher, top in tact, and then putting it in the cabinet. Oh, it was all I could do to keep my dinner down!!
Personally, if it is smelling, I would throw it out.
M.