It's definitely coming on for a reason. But then apparently the fault goes away. Get the code read and see what's causing it. It could still be an EVAP code for somewhere else in the system (do you happen to know what they fixed last time?)

I personally don't like having the check engine light on (or any dash lights) on, and I freak out if it does come on even though I know it's usually for something minor. But being stranded without warning isn't fun - if the car needs to tell you something else is wrong.