Did you install the game from a virtual drive? If so, uninstall and re-install from the drive you want to use to play the back-up copy.
Most recent safedisc protected games are "hot-wired" to run only from the installation drive (unless you do some registry hacking).
Other things to check:
Do you have clonecd's hide cdr media running? If so, your copy won't work because it's blacklisted by sd 2.9.
Are you trying to run the game from a writer? If so, make sure you have the latest version of alcohol installed (to beat the blacklisting) and that Ignore medis type is enabled.
You might also make a further image of the cd using alcohol's native mds/mdf format. If you intend to burn images with alcohol, there is no reason to use anything other than its native format (except where you want to patch an image of a securom 4.8x protected cd with twinpeak and, obviously, that doesn't apply here).
Your writer is quite capable of making working copies of sd 2.9 protected cds with alcohol.