Your code is defective as it assumes you get a command byte first - this may not happen in real life! I would suggest you implement a finite state machine like this:
[PRE]
switch(state)
{
case 0: //wait for command
if SBUF = MIDI_NOTE_ON
{
state = 1;
}
break;
case 1: //got note on command, expect note value
note = SBUF;
state = 2;
break;
case 2: //expect note on velocity value
vel = SBUF;
//store note and velocity
state = 0;
break;
}
[/PRE]
Please don't tell me you don't understand C language! The above is simply pseudocode and translates nearly one to one into assembler. The switch construct can be implemented with a string of CJNE.

As for the issue with the indirect operations, I'd suggest you use a simulator to step through your code and the problem should be obvious to you.