MissG,I noticed the "choppiness" to Up the River, too---something which may have been TCM's fault because earlier a poster at the message boards over there noted the same thing occuring during Meet John Doe.
The choppiness of the print looked like it was in the print. There were too many jump cuts (splices) indicating lost or excised footage at some point. Even the ending seemed very abrupt.
The choppiness made the film hard to watch for me. I did enjoy seeing Bogart when he was so young and I did enjoy the interaction between Tracey and Hymer, especially when they are leaving Bogart's mother's house.
The print may be all that exists. Fox had a huge vault fire in 1936 that destroyed not only most of their negatives but their fine grain duping negs as well.
It was after this devastating fire that Fox learned the valuable lesson of not storing their negs and their fine grains in the same location.