[SOLVED]
No I didn't have EOS Utility open (& in fact I had previously uninstalled it to prevent it opening every time I turned on the camera), but it did give me an idea based on another Canon related thread with a similar problem (http://forum.mainsequencesoftware.com/t/canon-60da-download-issue/198/9)
I couldn't find a way to control the mirror lock in EOS Utility, but I did recall that in the camera setting dialog in SGP (next to the device connect button) there is a field to set "mirror settle time". I had this set to zero (default) and changing it to a non-zero value fixed the problem! I have always set this to "2 seconds", and for some reason (after setting up the new equipment profile I guess), it had reverted back to "0".
I'm pretty sure that this is THE cause of the problem. I'm not sure if it's a limitation of the Canon DSLR mirror-lock system, or a "feature" of SGP, but it's good to know!
Thank you for your suggestions.
Kind regards,
John