first of all, if you are going to name people in questions, please do not post the same question on multiple forums, it is irritating either to have to answer twice or to ignore a question altogether.
I cannot say I have had any problems in the sequencer, with auto or manual punch.
The error message 22 is described on page 181 of the manual. This happens because you have pressed stop instead of rec stop in the screen, as decribed on page 84.
The other error message you decribe is number 56 on page 182 of the manual. This happens because you have pressed cancel in the screen before the punch out measure you have specified has played through as decribed on page 85.
Punch recording is only used to edit within the confines of the existing measures of a song, it is not used to lengthen a song. Lengthen a song by copy and pasting the control track, to put the correct stop commands before your punch out point, then you can punch in to your hearts content.
R1 and R2 are the "live" playing keyboard parts. If you want to multitrack record R1 and APC/Control first, then real time record any track you like with any part you like assigned on top.
If you want to record another part before R1 or R2 (for whatever reason) record it on R1 and then copy it out to another track, and then wipe R1. It is all in the copy and paste menu and very simple to do.
Alternatively just record the chords and control track with nothing on R1. Then you can multitrack on any other track or part.
Remember you are using APC in technics mode, not midi mode.