Also consider out-of-memory problems. Adobe is not known for being the friendliest of programs when it comes to memory usage. Adobe is a memory hog!
It could simply be that Adobe is hogging up all your memory and there isn't enough left over for Silverfast to do its job with.
As you say, Silverfast works well when it is used stand-alone. This would tend to rule out problems with the scanner or with Silverfast. If everything else on the computer works as you expect it to my focus would then be on Adobe and whether it is "playing nice with the other children."
Go to your System Profiler (Apple > About this Mac... -- Then click on the "More Info..." button.) See how much memory is available in your computer. Don't just go by what you remember. It is remotely possible that you have some failing memory. Using System Profiler will help verify that the computer is reading all the memory it's supposed to be.
After that, go to Adobe PS and see how much memory it's set to be using. (Photoshop > Preferences... > Performance) Don't let Photoshop use up more than 50% to 70% of your available memory. Adjust memory settings accordingly. Try lowering the settings so as to allow more free memory for Silverfast to run properly.
While you are there, check your scratch disks. Be sure you have enough free space on your scratch disks. Clear up some space and/or re-designate a new scratch disk that has more space on it.
Update/repair system permissions: /Macintish HD/Applications/Utilities/Disk Utility -- Then choose your main hard drive from the list on the left panel and click on the "Repair Disk Permissions" button.
Many people say that it is smart to repair permissions two or more times in a row until the computer comes back and says, "Permissions OK..." two times in a row. (Personally, I'm not sure about that.)
After that, check your installation of Silverfast and/or Photoshop. Reinstall if necessary.
If you're still having no luck, I would do something similar to what Rudeofus says. A full system checkup might be in order.
(P.S. - Holding down the "C" key during restart tells the computer to boot from the CD drive instead of the internal hard drive.)