Just a quick update in case others are experiencing similar issues.
I plugged the primary SSD HDD into the RR2340 and flagged it as the boot device in the RR2340 BIOS, checked the S1200BTS BIOS and made the RR2340 the primary boot device and I got the same result. It makes no difference what is flagged as the boot device as soon as any device is detected on the RR2340 the server will not boot, regardless of what boot settings are put in the Intel BIOS. It also seems that the Intel BIOS automatically detects what is plugged into the MB and changes its settings ignoring what the user had put in. For example I disabled the RR2340 in the Intel BIOS but as soon as I unplugged the SSD HDD from the Intel MB and put it in the RR2340 the RR2340 magically reappears in the Intel BIOS as the primary boot device.
I have resolved the issue. For some reason the Intel S1200BTS board keeps taking information from the RR2340 BIOS and resetting its boot priority. After using the hptflash utility to reflash the RR2340 BIOS with EBDA and INT13 disabled everything works great.
So for anyone out there wanting a 16 port RAID card to work with the Intel S1200BTS MB I have tested it and it works with Windows Server 2008 R2, with the driver downloaded from the HighPoint Global site and with EBDA and INT13 disabled on the RR2340 card.