I presume (since Amtrak does need to hit its Stockton ACE Station stop) that like some freight trains it's switching to the old WP line at Haggin, just east of the Sacramento station. The connection there isn't very good for east-west to southbound moves (or vice versa), hence delays. Plus, the old WP line is probably full of detouring freight trains too == more delay. And it's kind of slow anyway through midtown and south Sacramento == more delay. And remember, this only affects the 2 San Joaquin runs each way that go directly to Sacramento instead of Oakland; the other 4 each way are running normally, as are their bus connections to Sacramento.

Should be back to normal by this evening if UP's press mouthpiece is right.