I am now clutching at straws with this!
I thought that the GPU enhancement (enable open GL drawing) within Photoshop may be the cause of the difference in colour.
I opened a file scanned by the Flextight scanner, in Photoshop with the GPU enhancement switched off and then switched on.
Unfortunately there is no difference in the colour.
This appears to be a similar problem to what is being discussed in this thread (although with a different programme)..http://www.luminous-landscape.com/forum/index.php?topic=62029.0
I have to admit that just like "ippolitois" I am not smart enough to figure this out, so any help would be appreciated.