In our experience the P0888 will come back after you drive a bit. Get the car warm and rev above 2500 rpm for some time, then it shows up.
Also, there is the possibility that your scan tool will miss the code. Mine is intermittent sometimes. There are actually two computers responding to the error code query from the scan tool. One is the ECU and the other is the TCM. So some scan tools will miss the TCM response, which is the bad one. But a proper scan tool implementation will always get the TCM response...
A poor scan tool will only expect a single response to an OBD query or only have enough memory to store one response. However, the OBD protocol allows multiple responses and they can come back to back very quickly.
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