Something's missing...

There is nothing missing. Toyota relocated the flapper valve to the tank inlet in 1997 or 1998. Other makes, like GM still puts the flapper valve at the filler.
As far as your check engine light, unless you know for a fact that the gas cap was loose, you really need to use a scan tool to see which module set what trouble code(s).
For a loose gas cap, the check engine light may need a few days to a week of normal driving before turning off. The on-board diagnostic has to run and pass three consecutive times to turn off the light. For most evap codes, that means at least 3 warm-up cycles. Cold start, drive until normal operating temp, park at least 5 hours, repeat two more times.

 

Like the top poster said, that is completely normal.

 

Although the light goes out the code is still set so after it is read it should be cleared. In NJ that would cause the car to fail inspection.

 

In general, most ECM DTC's will clear from memory after passing 40 diagnostic cycles. Misfire DTC's must pass 80 diagnostic cycles to clear. DTC's in other modules such as ABS and SRS may remain in history until cleared with a scantool.