Edit: Sorry, the initial response was off the top of my head, this is working as expected for me at least.
Combine the program file path with the document path on the same line like so:
start "C:\Program Files\FileMaker\FileMaker Pro 12 Advanced\FileMaker Pro Advanced.exe" "C:\Documents and Settings\MyUserFolder\My Documents\MyProject\My File.fmp12"
Removing Start at the beginning of the string is exactly what was required. Just goes to show that reading the instructions on these types of things does not always lead one down the right path. ;-0