The reason the 5" pipes from Home Depot don't fit just right is because they aren't the right type of pipe. (As others have noted, with a little bending you can make 'em fit.)
A 5" wood stove pipe, gas appliance pipe, and pellet stove pipe are actually all different sizes, as I found out the hard way trying to make something fit. The 5" single wall pipe sold at most hardware stores is for stove vents, not pellet devices.
The FEC100 is designed to use L-Vent pipe, according to the current manual. L-Vent has a stainless steel liner that is 5", and there are L-Vent adapters that will slide right onto the FEC100. (The liner also makes it more expensive than regular stove pipe.)
The problem is most L-Vent pellet pipe is 3" or 4" for pellet stoves, but I finally stumbled on 5" L-Vent here:
http://www.ventingpipe.com/5-inch-pellet-vent/c1549The "5PSA" adapter fits my FEC100 just fine, and the rest of the L-Vent pipe just connects to that.