I think that is occurring because ~= is used in cases where you want to set a text stimulus to be equal to the response from a previous trial (see Using a Subject's Response as a Stimulus in the section on Input Files > Stimulus in the user's guide for details). I haven't encountered this before, i.e., where one would present a single equals sign as a text stimulus. Since DirectRT is apparently having trouble understanding this, you can try inserting a space before (and after if centering) the equals like this:

~ =

I just tried it and it seemed to work ok.

-Blair