i think because he doesn't remember going thru the gate. when ed talk to izumi abt the "truth", Al doesn't seem to have any clue because he doesn't remember.
once he remembered, he doesnt need a circle to do alchemy.
In the manga Al starts to remember the gate after Martel was killed inside his armor (which happens much much earlier in the manga than the anime) and begins to be able to use alchemy in the same manner is Ed.