Only the First Page Scans
If you're scanning through a sheet-fed scanner and only the first page has anything on it, you have three things to try, in order of effectiveness:
Switch Scanner Driver
On FileCenter's Scan dialog, go to the "Scanner" option and click the little "..." button there. This will pop up a list of every scanner driver available. If your scanner shows up there more than once, try each option.
(Note that while we usually discourage the use of drivers that begin with "WIA", in this case the WIA driver might work better).
Scan through the Native Interface
On FileCenter's Scan dialog, you'll see an option called "Use Scanner Dialog". Select it, then click "Begin Scan". This will make your scanner's native interface pop up. Proceed with your scan from there, making sure that the multiple-sheet options are selected if there are any. Often scanners get finicky about you scanning through their interface.
(If this works for you, go back to FileCenter's Scan dialog, select "Use Scanner Dialog", then click the little "Save" button right above it. This will make that setting the new default.)
Change the "Mode" and "Transfer" Settings
On FileCenter's Scan dialog, you'll see options called "Mode" and "Transfer". Try scanning in each of the different "Modes", then each of the "Transfer" type in each "Mode". You may come up with a combination that works.