@DavidW, did some reading on old threads and tried to fix it myself. I just tried installing onto a totally clean BG2:EE downloaded install via Steam, with V28 SCS for windows, no other mods. Prior to doing this I verified the install in steam, no missing files.
When installing the initialise component of SCS (which I'm guessing runs everything) I get the following various errors:
ERROR Installing [initialise mod (all other components require this)], rolling back to previous state
ERROR: Cannot perform auto-update, going ahead anyway! Sys_error("setup-stratagems: No such file or directory")
ERROR: Sys_error("strategems_external/workspace/temp_file2: Invalid argument")
ERROR: Failure("unknown function: clone item")
Again, thank you for any help you can provide.