There seem to be a few issues with the spawn timer. When you join a game or die, sometimes clicking the spawn point doesn't toggle it. Make sure every time after you die, you press M to bring up the spawn point selection, and then make sure the one you want turns orange (instead of staying blue) and then click "done."
As DFDelta mentioned, you have to click the left mouse button after you close the spawn selection screen to be put into the spawn queue too, although that was not clear to me until now (I just clicked randomly, because I knew something was up).
As soon as you do both of these, you should see a spawn timer go for a few seconds before spawning.
