You need to check that you have the correct settings in your Shipping/Packing in your admin area Configuration > Shipping/Packing
review your settings, the default settings shows that items with a weight value of 0 are free post, this is a bit of grey area for me, but by setting the weight on your products you want to free post, i would set the weight to 0 and where you was checking a tickbox for free postage i would leave that on the normal setting
Rob



