How do I prevent OS X from opening apps on external backup drive?

I have an external backup drive connected to my iMac and powered on 24/7. I do a nightly clone of my boot drive to this backup. I've been having a problem lately where OS X will open an application that is on the external clone of my boot drive instead of the internal boot drive itself. One example of this is when I use Lightroom and choose "Edit in Photoshop", instead of opening Photoshop on my iMac boot drive it opens it on the external clone of the boot drive.
Is there some way I can prevent OS X from "seeing" the applications on the clone, and opening them? Thanks.

Hi,
In System Preferences > Start Up Disk is one device set as the Start Up Disk ?
It may not be clear just looking at the left to right scroll area (depending how many drives and Partitions) but selecting one can often help.
At Start Up the computer looks for a valid Boot Disk.
If it does not seem to be set it is supposed to go through some checks to find out which one to Boot from. Most occasions it will pick the last Drive/partition that it was Booted from. However the order in which the Internal Drives are connected to the system may also pay a part, particularly of the Current required Boot drive is not the original hard drive (Or at least in it's physical place, cable connection-wise).
Also Click on the desktop and open Mac Help (Help Menu in the Finder) and see what that has to say.
11:30 AM Thursday; August 26, 2010
Message was edited by: Ralph Johns (UK)

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