I printed one of the boxes a couple of months ago. Everything fits really well. The LCD screen will be tight in the hole provide, the Arduino holes are spot on. You won't be able to use a GFIC outlet though. So make sure you have one of those upstream from the controller.
Search for a spreadsheet titled “electric heat.xls”. It’s great for planning your electric brewery. Answers questions about how long it will take to get to a certain from a certain temp, etc. I found it valuable in assessing what element to use.
Get out your voltage meter. If you don't have one, get one for cheap at your local electronics store.
The voltage that switches the relays is DC. The relay is switching an AC circuit. There's a pretty big difference.
This actually sounds like the SSR might be stuck in the closed position. If you have a spare one, swap it out and see if that doesn't resolve the issue.
Worthy of mention - make sure you buy a quality micro SD card (like SanDisk) for your PI's hard drive. LOTS of issues raised by using a PI is due to a corrupt SD card that can't handle having the power being unplugged/plugged in. ALSO make sure you have a good process to back it up AND restore...
Trace the power lines from the input to the PIDS.
Are switches working ok?
Do you have a multimeter with which to check the voltages and connectivity of wires and components?
Pictures of the inside would be most helpful.