Yes, water in a connector is shorting it out.
The ECM is going into default mode to protect itself. It is reading a high resistance somewhere and is going into default.

----- Gimpster -----

 

But the only thing is, i have not been able to ride it, i just put the motor back in sunday, and it has been in the shop every since.

 

If you pay attention to the blinking there is a slight pause.... count the blinks between the pauses.

 

Not always, ECM failure or a bad/shorted speed sensor will make the display constantly flash. Some times a bad gear position switch can be bad in more than one place and it will trigger the flashes constant.
The ECM can store like 9 codes but only will display a few at a time. Once codes are brought up and then removed, the next ones in order will display until up to the 9 codes are removed. So just reading codes once and removing them may not be curung the issue. Or should I say once you clear the codes once, more codes can appear although there is nothing wrong with the unit. It just has more codes stored in the ECM that were never removed and are surfacing once the first set flashing on the display are removed The process must be done multiple times. Odd as it sounds I have had units with 9 codes in them and they will continually flash with no pauses on the display.

edit:
500rubicon, you should disconect the shift control motor and clean the connection there first.

----- Gimpster -----

 

So how exactly do you erase the codes the up and down buttons??

 

blake3612 -
You should start a different topic about your rubicon
Trying to help 2 people with simular issues, but yet different, in the same thread gets confusing
Your Rubi was not submerged and may have different issues although it is constantly flashing the same

----- gimpster -----

 

ok I will start one sorry new to all this

 

ok sounds like the same problem i have had now 3 different times, its the angle sensor which controls the whole electric shift and yes only 1st gear works and reserves sputters, angle sensor is $86 and its simple to change but jus a lil tricky reseting the computer after u install it, cheak out page 3 or 4 for angle senor intiail set up procedure

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06 Honda Rancher 400AT, 2" lift, 26/12/12 mud lites rear, 26/10/12 mud lites front, ITP chrome rims, HMF slip on pipe, exhaust wrap, K&N filter, outwears prefilter wrap, Dyno jet kit, customized snorkle with differential and carb vent lines ran up with snorkle, 2000lbs superwinch, warn front bumber with warn trail lights

 

i have a 2005 Honda Rancher AT and the Esp is flashing and it flashes 12 times what does it mean? is sputers when i put it in R but when i put it in D it doesn't come out of first gear.

 

<div class="FTQUOTE"><begin quote>Originally posted by: usajoemiller2005

i have a 2005 Honda Rancher AT and the Esp is flashing and it flashes 12 times what does it mean? is sputers when i put it in R but when i put it in D it doesn't come out of first gear.</end quote></div>

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First check/clean & put dielectric grease on all of the couplers (connections) for the ECM , shift switches , shift control motor , etc.

Code #12 is "ECM motor driver circuit" .. Do all the tests below