I had the same problem.
Solution:
go to /Library/Application Support/Quake3/baseq3 in your home
there's a file named q3config.cfg
edit it and change the key binded for toggleconsole.
There may be more then one command bind ~ "toggleconsole" in the config: it's an error of Q3, delete them except for one.
I use k. Save and run Q3A.
That's all.