Can this problem with the IAC be fixed?

Hello. I'm using an ear training program like EarMaster 5 and i'm routing it with IAC in Mainstage because the souds of EM aren't very promising. As long as i practise with a piano sound everything is fine. But when i change sound in Mainstage (say an organ) it doesn't play me the first tone. It always with no exeption skips the first tone of the arpeggio that EM plays me and starts from the second tone. The funny thing is that Mainstage shows that the first tone is received, it registers it in the toolbar, shows which tone it is, but it doesn't play it. This hapens with mabye 70% of the sounds in mainstage. Why is this happening?