Check engine light. WTH
Not sure about on the JK specifically, but I know some vehicles only run some of the EVAP tests when the tank level drops down to around half or less. Sounds like this could be what's happening, but you should pull the code to confirm.
X2- this will give you your fault code. look it up online. actualy quadratec has alist of all the fault codes i believe and start troubleshooting from there.
good luck. sounds like you might be getting an evap related fault



