If shaft speed sensor was faulty you would have a trans fault all the time. It's just a magnetic sensor located to read off of a toothed wheel.

Trans do better when it's cold (relatively speaking, like on a morning start off vs. after driving)?

The slip and fault happen whether in manual mode or auto? (note: manual mode isn't manual, it's just a way for the driver to respectfully request a different gear. Changes are still regulated and approved by the computer committee.)