Lipo's will puff a little if not stored right. They will also puff if left under volted.
If you're not using them for more than a week, you need to take them down to half voltage and store cool, like in a fridge. A lot of new chargers do have a storage function on them to balance them down to the right voltage.
Also if you're running them to where the speed controller shuts down you're probably under volting them even though you may have a cut off on the speedo. Stay away from draining them down to full capacity!
Give it a couple of charge cycles and then store it cool as sometimes the puffiness will go. Charge outside and somewhere safe just encase it is on its way out.
Ps If you do store them in a fridge, make sure they do not freeze.