C# on Alto Saxophone NEVER WORKS!!!!

This program had the potential to be very useful for arraning for a small jazz combo I'm in, but I needed to hear how it would all sound together. I've read through the Local manual, and somewhat understand the program, but the middle C# on the Alto Sax(concert E) Doesn't work!!!! It works in the High and Low octave, but not the middle! I am currently looking for another free program to arrange on, that would be a bit better, as this program has annoyed the hell out of me, as E is one of the more important notes I use in alot of arrangements that are in Concert C, and not having that note really ruins the program for me, as I use the Alto Sax alot.