What setting did you use on the Filter Dialogue... I generally scan with "none" rather than "Auto Sharpen" or any of the other settings, which, admittedly does leave the scans rather soft, However, I'd sooner take charge of the sharpening myself in CS5, usually using a High Pass filter layer, as I find I can sharpen the image up without exaggerating the grain structure.
It took me a couple of rolls of film before I got the hang of the batch scanning - the fact that you CAN change settings for individual scanned frames can actually be useful - especially if you're working through a bunch of old negatives, some kodak, some fuji, some ilford... It's also handy to be able to scan all the shots on a negative strip, but just do the obvious duffers at 800dpi, while the better ones get 4800dpi say. I do wish that there was an option to select a single frame and say "Apply these settings to all" - maybe something to feedback to the writers.
Also - new film profiles are issued with update releases of the software, so don't forget to keep up to date on that score... the version shipped with my 8800F was well behind the times - current version (presuming Silverfast SE) is 6.6.2r2 I believe...