1999 Oldsmobile Silhouette rough shift

My car has been regullarly serviced, including transmission flush every 50K miles. The transmission operates smoothlly and efficiently as new most of the time, however, after being driven some distance in stop and go or hilly conditions the shifting becomes noticeably rough. If I stop fior a short while, it behaves normally, sometimes for the rest of the day. What can cause this, and how much should I expect to pay for repairs?