If the hard disks are configured as SATA ahci - they are seen by the loader but install does not see/use the second 
drive.
With the BIOS set to ATA mode both drives are usable but very slow.  Install with type 179 took over 14 hours (Started 
about 1200 and went to bed about 0200 next morning).  The QNX6 file system preparation was still going at 0200.   Next 
day after I got the prompts for the file system, the copies from /cd to /hardisk took over 5 hours.   It reminded me of 
the very early QNX4 system which let the CD shutdown between reads.   The HD activity led was flashing about once per 
second.

Because of other bad results, a couple of days later I did a re-install using type 79 (QNX4).   The only improvement was
 that the file-system preparation type was insignificant - again - I went to bed before it finished and again - the 
copies took more than 5 hours.

sloginfo is full of 
Dec 16 08:38:11    2    19     0 eide_reset:  complete 302 ms
Dec 16 08:38:11    2    19     0 eide_init_devices: ST9320421ASG path 2, tid 0, udma -1, mdma -1, sdma -1, pio 4, mblk 
16
Dec 16 08:38:11    2    19     0 eide_reset:  complete 301 ms
Dec 16 08:38:11    2    19     0 eide_init_devices: ST9320421ASG path 2, tid 0, udma -1, mdma -1, sdma -1, pio 4, mblk 
16

 at the rate of 3 per second implying (to me) the drive is so busy resetting it has no time to do any work.

After eventually getting 6.4.0 installed using ATA mode, I reset the mode to ahci and tried to boot -
using the second hard drive (from the BIOS F12 option) no QNX loader on the first drive.

Press F1-F4 to select drive or select partition 1? 1
Hit Esc for .altboot...............................................................................
Press the space bar to input boot options or D to disable DMA...
Trying SATA ahci. Scanning for devices...
...found 2 devices
Trying EIDE. Scanning for devices...        <- what about the CD which is EIDE as reported in ATA mode
Trying USB. Scanning for devices...
Trying SATA mvSata. Scanning for devices...
/.diskroot file not found on any filesysem.
Starting with safe mode
Spawn of /bin/sh failed : No such file or directory

I cannot try 6.3.2 because the CD will not run - it complains of     no  /dev/pci

A report with more problems and pci/usb reports is in post18582@community.qnx.com but I will try to address the problems
 one at a time.

Warren