Really? I've been using 0.3.23 for a while and I've had to pay the transaction fee on every single transaction except for about 5/100. For me, the *rare cases* are when it doesn't make me pay a fee. Did something change in 0.3.24?
Care to share an example transaction so we can see why?
I can only guess you're making payments with outputs smaller than 0.01 BTC?
I made a ~6 BTC deposit and was prompted a 'minimum' fee of .03 ...