Right, got it all working. These are the steps I made and also how my Mac Pro is currently setup.
I have my Mac Pro with 120Gb Vertex 2 in Bay 1 and a 2Tb SATA drive in Bay 3 that has 250Gb Boot Camp Partition with Windows 7 installed on it. I also have another 120Gb Vertex 2 in Bay 2 ready for me to RAID 0 with Bay 1 but that's another story.
Important thing is, YOU MUST HAVE A WORKING WINDOWS BOOT CAMP ON YOUR MAC PRO. It's not necessary to have it on your precious SSD, just on one of your drives.
1. Run the Boot Camp Assistant and let it create a 5Gb partition (default) on your Vertex 2
2. Once it's created the Partition just click Quit and Install Later
3. You now need to format that 5Gb partition NTFS as it creates it in FAT32. You can do this 2 ways, you could boot into your current Boot Camp and format it in there OR you could install
http://www.paragon-software.com/home/ntfs-mac/ and format it NTFS (uncompressed) straight in the Disk Utility.
4. Now shutdown and Boot into Boot Camp, download the firmware from OCZ and run the utility. It will find the disc first time now without any problem. Once it's updated it (it only takes seconds) it will reboot your Mac back into OS X.
5. Run the Boot Camp Assistant and select the Remove a Boot Camp partition and then select your 5Gb partition and away you go, back to your full 120Gb and new firmware.
I would make Carbon Copy Clone before you do any of this mind you just in case. Mine went like clockwork but I wouldn't bet my house on it.
Good luck.