Quick update for you, yesterday I installed windows 2003 R2 on the G6 after installing the drivers it could see the 29320lpe card fine in the OS and had no problems booting up.
I then went on the HP website and applied the following BIOS and firmware updates
Type: BIOS - System ROM
Version: 2009.10.01 (29 Oct 2009)
Operating System(s): Microsoft Windows Server 2003, Microsoft Windows Server 2003 for 64-bit Extended Systems, Microsoft Windows Server 2008 Essential Business, Microsoft Windows Server 2008 R2, Microsoft Windows Server 2008 Small Business, Microsoft Windows Server 2008 W32, Microsoft Windows Server 2008 x64
File name: cp011971.exe (1.4 MB)
Type: Firmware - Network
Version: 2.1.5.5 (10 Nov 2009)
Operating System(s): Microsoft Windows Server 2003 for 64-bit Extended Systems, Microsoft Windows Server 2008 Essential Business, Microsoft Windows Server 2008 R2, Microsoft Windows Server 2008 Small Business, Microsoft Windows Server 2008 x64
File name: cp011680.exe (4.3 MB)
Type: Firmware - Storage Controller
Version: 1.16 (B) (11 Nov 2009)
Operating System(s): Microsoft Windows Server 2003 for 64-bit Extended Systems, Microsoft Windows Server 2008 R2, Microsoft Windows Server 2008 W32, Microsoft Windows Server 2008 x64, Red Hat Enterprise Linux 4 (x86), Red Hat Enterprise Linux 5 Server (x86), Red Hat Enterprise Linux 5 Server (x86-64), SUSE Linux Enterprise Server 10 (AMD64/EM64T), SUSE Linux Enterprise Server 10 (x86), SUSE Linux Enterprise Server 11 (AMD64/EM64T), SUSE Linux Enterprise Server 11 (x86)
All of which are newer than those available on HP Firmware boot CD 8.6
After installing the firmware updates we reinstalled ESXi 4.0 HP version, this time the drivers for aic79xx loaded successfully
Once the installation had completed the server also appears to be a lot more responsive to VM client commands such as scanning the data stores editing guest VM's etc.
I have also updated the firmware of the Adaptec 29320Lpe from 4.31.4 to 4.31.9, I have not attempted to try the HP SCSI card I will do so later to see if it has also resolved the mpt driver issue but I think we will keep the Adaptec card in this server as it is on the HCL
It would appear the system BIOS on the 8.6 Firmware CD from HP was the original cause of the error.