I have an Intermatic T104R timer set up for my pool pump. It seems that the clock is running backwards. Why is that?

If dial is not rotating clockwise and keeping correct time on 240Volt T104 timer, then WG1573 clock motor is probably bad.

Open following link for troubleshoot checklist:
http://waterheatertimer.org/How-to-troubleshoot-Intermatic-timer.html

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Direction is controlled by a gear inside the timer motor cover. When you open the Intermatic door (T100 series - mine is the 220v T104) look thru the circle near the top (use a flashlight) to see the little black gear in the back turning clockwise. If it's going CCW it's running backwards. Turn off power (breaker), unsnap the mechanism (release is at the inside top) and pull the guts forward to access the timer (careful of wiring). The timer cover cap (with the printing on it) can be carefully pried off with a sharp blade or pocket knife. Inside, the 1" gear on the right can be lifted up, turned ? 180? and set back down. The position of the metal lever bar on the bottom side of this gear forces the magnet wheel next to it to go in the proper direction. The lever bar will turn with the gear, until it contacts one of 2 plastic posts. Whichever one it was against, reposition it so the bar turns toward the other plastic post. Mine was running backwards because I took it apart to inspect it (worn gear) and when I modified it to engage with the unworn part of the gear, I (mistakenly) installed the 1" gear in the wrong position, then had to figure out why it was running backwards. This position can't change by itself, so I assume your has ALWAYS run backwards. Running backward WILL cause the timer to bind up when it contacts the adjustable timer tabs. Check clearances of power wires before turning power back on to make sure nothing is shorting. (Reversing the wiring to the timer should not make any difference on an A/C motor.)