I've been having the same problem as OP. I've also tried "Print as Image" but unfortunately it hasn't helped. Still get blanks.
OSX 10.10.3, Scansnap s1300i, Scansnap manager 6.2 L22, Canon MP480 printer, Adobe Acrobat Pro DC and Acrobat Pro 9.5.5, iMac 2.93 GHz Intel Core 2 Duo.