Recording Multitrack

When i have a multitrack score and i want to record each part separately one by one using the onscreen keyboard or a midi one, for example I selected the two measure count-in to be ready to play the part and after I recorded the trumpet part then I want to start recording the alto sax part within the same score while the two measure count-in is happening the trumpet part that I already recorded start playing before the count in finish not allowing me to record the sax at the same time while the trumpet plays. By the time i can start recording the sax part, the trumpet part is already playing two measures ahead. THAT DOES NOT MAKE SENSE