I can understand your frustration in not getting an answer the first time you posted this question.
I think that the reason you did not get an answer is that no one here knows the answer. As I understand things, the AHCI has something to do with SATA, which means a disk driver. If your setup does not have a SATA drive you could try creating the .boot file with out the SATA driver. Otherwise you probably need to talk with QNX about this. If a driver works with the non-smp kernel and but doesn’t work with the smp kernel, it suggests a serious race condition problem in the driver. If this is the case, I’m sure QNX will have a concern as well as you.
I did run into a similar problem a while back. The Adaptec SCSI driver I was using under QNX 6.2 caused a kernel crash on the server I was running with the SMP kernel. The eventual upgrade to 6.3 vanquished the problem.
One last thought, I just read that apparently AHCI can usually be turned off in the BIOS. The context for this posting at wikipedia.com was that with WIndows 7, you want to turn AHCI before you install as turning it on afterwards can cause problems.