Replaced intermatic wall timer with GE timer - Lights won't go on, however when turning on the second switch for the outside lights they flash on and off

1) You performed correct troubleshoot steps down the line.
Last thing would be to install defect timer on another light circuit in house, and see if problem is the timer or wire going to coach lights.
http://waterheatertimer.org/pdf/Intermatic-ej351c.pdf
http://waterheatertimer.org/Intermatic-timers-and-manuals.html

2) EJ351C has 1 year limited warranty.
Buy new EJ351c and install single pole light switch until timer replacement is available.
Timer has easy 2-wire installation. Turn off power. Connect new timer just like old one was connected. Either timer black wire connects to either wire in switch box.
http://www.smarthome.com/25077/Intermatic-EJ351C-24-Hour-Mechanical-In-Wall-Timer/p.aspx
http://www.amazon.com/Intermatic-EJ351C-Programmable-Mechanical-Security/dp/B000Q9YUGU

You probably need new set 156T1978A tripper.
Trippers are made of softer metal and are designed to wear down and be replaced so timer lasts decades.
http://www.grainger.com/Grainger/INTERMATIC-Timer-Tripper-2E054?Pid=search

Open following link for troubleshoot checklist: line 4 applies
http://waterheatertimer.org/How-to-troubleshoot-Intermatic-timer.html

1) GE 15086 is not a 3-way timer.
GE programmable timers are for single-pole switch replacement only. I have tested this timer, and own several GE timers, and many other brands.

2) Open following link to identify timers that work for 3-way switching.
http://waterheatertimer.org/GE-timers-and-manuals.html#15071

3) After buying correct timer, then you need to review wiring diagrams carefully because the timer replaces 1 of the 3-way switches, but other 3-way switch has to be wired exactly right to match your brand of timer.

4) Links on page above show manuals for each of the 3-way timers. Compare wiring for each timer with Intermatic wiring that you are replacing, because Intermatic is wired differently than Aube.

5) Or just buy another Intermatic ST01C or EJ500 or EI400, etc, and wiring with change out 1 for 1.

6) Add a comment for more free help.
Also take advantage of fixya expert assistance live.
For a price, expert works with you while you work on timer or any do-it-yourself project.
Fixya is always less expensive than a service call.

If the timer is setup, you can press the MODE button until it shown MAN.
Press on the door of the switch timer for on & off.
You can printed a pdf manual at this site.
Click on English under Instruction Manuals
Also there is an Easy Set Instructions under Supporting Documentation.

http://www.intermatic.com/products/timers/consumer%20indoor%20timers/in-wall%20timers/ej500c.aspx

I test these timers.
GE 15071 timer has internal clock that runs on electricity. That's why timer has extra wire.
Intermatic, GE, Tork, Leviton, Sylvania, Woods, Utilitec etc in-wall timers each wire the same way.
The only tiny difference is GE doesn't have green ground wire.
http://waterheatertimer.org/Program-wire-Utilitec-0192773.html

Here's what to do:
1) Old switch has two screws (excluding green ground screw)
One screw on old switch has 2 black wires >> these are hot wires > timer black wire connects to these hot wires. This will power the timer.
2) The other switch wire connects to timer red wire. This will send timer signal to lights.

3) Timer white wire is for the timer clock.
Timer white wire connects to other white wires that are twisted together and covered with wire nut >>> these are neutral wires, and now timer clock will operate
4) For EZ connection to other white wires, strip back another inch on timer white wire so stranded wire can wrap like a candy cane around solid copper wires. Then twist wire nut on very tight.

5) When wiring is complete, push door on timer for manual override. Lights should turn ON-OFF. If lights do not turn on, reverse timer red and timer black wires. Make sure outdoor bulbs are working.

Add a comment any time

If you have a battery operated timer like Intermatic ST01C, it may not operate another timer.
The ST01C will not operate circuits farther away than 100 feet, or operate when wires are located underground. Sounds peculiar doesn't it.
I assume these parameters are because of how the battery interacts with electronics inside the timer.
On the other hand, maybe your battery is getting weak.

http://waterheatertimer.org/Intermatic-st01c.pdf
The manual shows incandescent, fluorescent, motors and DC loads.
But manual doesn't specifically include or exclude other electronic devices that might put electronic feedback on the line.

I'll run a test on the ST01C next couple days, and post result on this thread.

noop means no operation.
This usually shows on older timer.
You posted under Intermatic ST01C.
Other have written to fixya with same symptoms.

CR2 battery might be bad. Replace battery.
Replace battery quickly and current time remains in memory.
Battery out of timer longer than 30 seconds, then current time and day disappear.
Programming remains inside timer forever with or without battery until timer is reset.
Others report they changed battery and timer never came back to life afterward.
http://waterheatertimer.org/ST01C-program.html#battery

Manual troubleshoot section also suggests resetting timer, and then re-programming.
Manual:
http://waterheatertimer.org/Intermatic-st01c.pdf
To reset timer, hold down ON-OFF button and push small round reset button with paper clip.
Push reset for 3 seconds and release.
Keep holding down ON-OFF until INIT shows on display.
Release ON-OFF and wait for display to show.
If display never shows, then battery is dead or timer is bad.
ST01C comes with 1 year limited warranty.

Advantage of Intermatic battery operated timer is simple wiring, plus astronomic function (dawn-dusk).
All in-wall timers have advantages and disadvantages.

Nextag shows new ST01C sellers
http://www.nextag.com/intermatic-st01c/products-html?nxtg=90ff0a280507-C4F7FB4C58223A3F
Page also shows Intermatic EI600 astronomic timer that comes with 5 year limited warranty

I answer questions for free.
I specialize in timers and electrical devices

Below is the manual for the EJ351
http://www.intermatic.com/~/media/files/intermatic/products/instructions/timers/ej351c%20-%20english.ashx
The red light is a good indicator of the EJ351 timer.
The manuals says that you can clear all programming by moving control lever to OFF-CLEAR position for 20 seconds.
After programs are cleared, the red light will turn off.
Then move control lever to ON position, and then red indicator light will start flashing.
So the problem may be that the timer programs were accidentally cleared.
Use the instruction manual to re-program your timer.
Add a comment if you need more assistance, and I will help.

EJ341 has 2 wires

this is a common item. I would try a home depot or lowes first then an electrical supply house. or go on line to intermatic.com