I myself just installed BS2 this morning, I couldn't assign Pro Pedals to first mention of Brakes in the axis list.
Went ahead and assigned left and right wheel brakes. It did recognize and assign the left and right peddle brakes. I see no problem, seems acceptable to me.
BTW, most times that I tried assigning commands to axis, I usually had to try multiple times to get BS2 to recognize them, but did get assignments accomplished. (one thing I noticed-- If I remember correctly, in BS1, you only had to move axis in one direction, In BS2 you have to move axis in both directions to get it recognized) just saying.