Can I wire my heater to my pool pump timer. I want power to the heater only when my pump is running.

http://waterheatertimer.org/How-to-wire-Intermatic-control-centers.html

http://waterheatertimer.org/Intermatic-control-centers-and-manuals.html#RT3

RT3 series has T104 240 volt timer -or- T103 120 volt timer, -plus- low voltage transformer for pool light.
The circuit breaker can be used for transformer, or another outlet or nearby light etc, or it can be used for a T103 120 volt timer.
To trace the wire back to breaker box.... open you main panel and start turning off breakers one at a time and label the panel.
See if you have single breaker or double breaker supplying power to pool equipment.
Gene

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T101P3 is ordinary 120Volt T101 mechanism inside a beige plastic box.
Rated 40 amp.
Three terminals A 1 2
Very small white wires that power the WG1570 clock motor are connected to terminals A and 1.

White neutral wire from breaker box connects to terminal A
Black Hot wire from breaker connects to terminal 1.
This will power the clock motor, which will switch the timer on-off.
Green ground wire and bare copper wires connect to green ground screw.

115volt motor should have 2 wires.
Connect white wire to terminal A
Connect black wire to terminal B
http://waterheatertimer.org/How-to-wire-T104-Intermatic-timer.html#T101

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Question posted under Intermatic T104 series timer and pool control center.
Open following link to see how to set this timer:
http://waterheatertimer.org/pdf/How-to-operate-and-set-T104-timer.pdf

Intermatic T12404R control center has 2 timers.
Each timer is set same way.
Timer must be reset after power outage. If time dial is not rotating correctly or is sticking at the tripper, then the WG1573 clock motor can be replaced by homeowner.
Both timers are 240Volts, and can be wired in variety of ways to control different voltages. For example 120Volt pool lights, and 240Volt pool pump and pool heater etc.
Each timer snaps out of control center using thumb spring located top inside box.
Each timer mechanism is sold separately. One timer is T104M. The other is T104M201.
The difference is that the 201 has a 'fireman's switch' that can be wired to pool heater, and the switch turns off heater 15-20 minutes before turning off pump.
Each timing mechanism can be repaired by homeowner using available clock motors and trippers.
http://waterheatertimer.org/Intermatic-trippers-and-parts.html#T100

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Sounds like the clock leads are on the wrong posts, or at least the hot one is. If if was moved to the load side then manually starting the timer will also power up the clock motor. As soon as the clock trips the off timer, the pump and the clock motor are both off. Examine the clock leads to the wiring diagram inside the clock box cover to ensure they are connected correctly. I bet you'll find one of the wires is misplaced.

John

Sounds like 240Volt WG1573 clock motor has gone bad and needs replacement. But more checking is needed.

You posted under T2100-4R which is 60 amp Intermatic control panel with a single T104M 240Volt timer mechanism.
All Intermatic timer mechanisms can fit into same control center, so you can possibly have different timer mechanism inserted into the T2100-4R control center.
The control center can have up to 4 circuit breakers.
Instruction manual shows that timer can also have fireman's switch that is wired to pool heater and causes pool heater to turn off 20 minutes before pool pump turns off.
http://www.poolandspacontrols.com/products/mechanical%20controls/60%20amp%20pool%20and%20spa%20control%20panels.aspx

(1) First thing: If you have T104 mechanism, do a troubleshoot run-down to see if trippers, clock motor, or wiring are suspect:
http://waterheatertimer.org/How-to-troubleshoot-Intermatic-timer.html

(2) Next would be to check the circuit breakers for loose wires, burned connections, or the smell of burning or crackling sound that says breaker is loose on the busbar.

(3) Check for loose wiring on T104 and test circuit:
http://waterheatertimer.org/How-to-wire-T104-Intermatic-timer.html
(a) Push the manual override lever to OFF position and test across terminals 1 and 2 and then across terminals 3 and 4 to make sure timer is turning off power to pump. Both tests should show 0 volts.
(b) Push manual override lever to to ON position and repeat test above. Both tests should show 240 volts.
If the test fails, then buy new T104M timer mechanism.

(4) If the T104 timer is turning off both lines in the 240Volt circuit, then pump cannot turn on since neither wire is Hot.
However if your T104 timer is actually a T101 timer or if timer has different wiring, where timer is turning off only 1 leg and not both legs of 240Volt circuit, then pump has one hot wire available and a short to ground could cause pump to turn on unexpectedly.

Check that your pool heater supports optional fireman's switch
Black wires on firemans switch connect to pool heater. Power to fireman switch comes from pool equipment and not the timer.
If pool equipment does not support fireman, then cap off the wires.

Fireman switch turns off heater 15-20 minutes before turning off pump.
The purpose is so pool equipment lasts longer.

You can buy the fireman's switch separately, but if this is new timer, then switch is probably good.
Open following link to identify fireman's switch and related parts for the timer:
http://waterheatertimer.org/Intermatic-trippers-and-parts.html#fireman

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Check that your heater isn't wired to the line side of the timer. It should be wired on the load side, NOT the line side. Problematic at best to have your heater powered all the time, at worst deadly to the heater should your various pressure/temp sensors fail and the heater fire up when the pump isn't on.

Another option would be to get an electronic timer like the Intermatic P1353 that has 3 circuits on it that you could program to cut on and off at different times. For example, you could have one circuit that controls the pump and turns the pump on, then the second circuit would turn on the booster pump at a set time after the filter pump had come on and then the heater could be set to also run at a preset time after the pump circuit was activated. Since the pump, booster and heater are all 220, it's a straight forward hookup with everything in one timer box.

The lights, as stated before, would be on a separate circuit (110) and have its own timer or photosensitive eye set in line.

You won't use all three wires from the heater, only the two required for the line voltage present inside the timer. Is the timer fed 115 or 230 VAC? You will want the heater on the line side to avoid the heaters power being interupted all the time causing you to have to always reset it. Just be sure to select the corect leads from the transformer based on voltage present.