Blank Pages aren't Removed
Blank page removal is based on the amount of white on the page. Or better put, it's based on your page lacking any black areas. If pages have more black than the letter "X" can encompass, the page won't be regarded as blank.
"Noise" and speckles on the page are a common reason the page might not be recognized as blank. Adjusting the black/white threshold when you scan can help here (you'll find it under the Advanced tab on the Scan dialog).
Even more common is a black line along the edge of the scan from the page not getting set straight or pulled straight through the scanner. This line is more than enough to keep the page from being regarded as blank.
FileCenter tends to err on the side of caution, preferring to leave questionable pages in the document rather than aggressively removing pages, with a potential for false positives.
However, you can adjust the blank page sensitivity yourself. Go to FileCenter's Settings > Scan and adjust the Blank Page Sensitivity, making minor adjustments until you're satisfied with the sensitivity.