The difference is in the kind of damage you are choosing to do with your flail.
The damage weapons (or fists/feet/etc.) do is calculated by Damage Classes (DCs). All weapons (fists/feet/etc.) do primarily either Normal or Killing Damage. With weapons that do primarily killing damage, you can choose to 'Club' your weapon, doing Normal rather than Killing damage. Your flail is a Killing Damage weapon, but you chose to 'Club' the ghouls with it, thus reducing the chance that you would kill them.
When you do Normal Damage (Stun Damage primarily) like you were doing with the Ghouls, each damage class equates to 1d6. The number you roll on the dice is the STUN damage, and BODY Damage is calculated by looking at each die roll (1=0 BODY; 2,3,4,5=1 BODY; 6=2 BODY) and on the average you'll do 1 BODY for every die you roll. There are other adjustments depending on your Hit Location Roll, your targets armor, etc., but that's where I get the base damage.
When you do Killing Damage (which is the default for your flail) it takes 3 DCs to equal 1d6 (DC 1 = 1 pip, DC 2 = 1/2d6, DC 3 = 1d6, DC 4 = 1d6+1, etc.) but the number you roll on the dice is the BODY you do, which is then modified depending on your Hit Location Roll to get your STUN damage. Because of the way defenses are calculated, Killing Damage tends to do more BODY damage than Normal Damage does.
With me so far? OK, now for the rest . . .
On page 3 of your character sheet, at the bottom right, is a list of Combat Maneuvers. Each of those maneuvers includes a Phase (which you can mostly ignore), a modifier to your OCV and DCV, and an effect. The ones you've been using (per my assumptions) are Martial Strike and Offensive Strike. Under the Effect column, you'll see that Offensive Strike says 'Weapon +4 DC Strike.' This means that you add 4 Damage Classes to the damage the weapon normally does. So, your flail moves from DC 3 (1d6 Killing Damage) to DC 7 (2d6+1 Killing Damage). There is a hard and fast rule that you can NEVER more than double the base damage class of an attack, so your flail is capped at DC 6 (2d6 Killing Damage).
Clear as mud now? It seems like a lot to figure, but believe me, once you've done it a few times it gets lots easier . . .
After you've absorbed this part of the lesson, I'll go into the Hit Location modifiers, and how they figure into Normal and Killing Damage.