I had the same thing happen to my H4 upgrade. Below is an old write up I help put together.
If you have a '97 and newer, with factory fog lights; this could help your situation...
Ivan
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Handlebars and I have been trying to tackle the same situation. He has the Painless Wiring setup, I have the Kolak Special wiring harness from a JU group buy. We've determined that they are basically the same kit. The common denominator between all of us is factory fog lights and late model ('97 and up) XJ's. What Handlebars discovered (and I confirmed with a VOM) was that with both wiring harnesses, the follow symptoms occur:
Low Beams on - works fine.
Hi Beams on - works fine.
Return to low beams after firing off Hi beams - BOTH Hi and lows are on!
Handlebars notice that if you remove fuses #3 & #4 from the distribution panel (which controls the now unused driver's side plug) at the passenger side kick plate, the hi and low beams work like they should. That is:
Low Beams on - works fine.
Hi Beams on - works fine.
Return to low beams after firing off Hi beams - Lows fine, hi's off.
Handlebars figured that the unused drivers side stock light plug was creating some sort of feedback from the fog lamp relays, which prevented the new wiring harness relays to kick open. Only kicker now is that the fog lights won't work because they operate on the same #3 & #4 circuits the drivers side plug...arghhh! Ok, so I had another theory. How about plugging the wiring harness into the driver's side plug, removing now fuses # 5 & #16 to disable the unused passenger side light plug; and maintain funtion of the fog lamps. I built a temporary jumper cable to reach the other plug to test this theory. Good theory, but it didn't work. Still wound up with this situation:
Low Beams on - works fine.
Hi Beams on - works fine.
Return to low beams after firing off Hi beams - BOTH Hi and lows are on!
Through all this, I did notice that if after you activate the hi beams and return to low beams, if you shut off the light
and turn them back on; only the lows will be on. This worked using either plug.
So your options thus far as follows:
1. Leave the fuses in, and just don't use the hi beams. Seems the lows are way plenty bright anyways; and you still maintain the use of your fog lights. If you want to use your hi's, when you downshift the lights to low; shut the lights off momemtarily to "reboot" and regain use of lows only (a pain).
2. Remove the fuses #3 & #4, lose use of your fog lamp switch and fog lights, but maintain full function of your hi and low beams without both staying on while switching back and forth. With this option, you'd have to run a whole different circuit for your fog lights to continue to use them.
Ok, now that you're done reading, there is a fix for all this though which Joe Furlong came up with (thanks Joe!). Thanks also to Handlebars for figuring out the fuse #3 & #4 issue......
After removing fuse #3 and #4 that controls the unused headlight plug (after installing a wiring harness), you can remove the fog lamp relay located in the distribution panel. You will notice that there are 5 spade type connectors on the relay. If you build a small jumper to by pass the relay, and plug the jumper where plugs 3 & 5 (as labled on the bottom of the relay) would plug into in the panel, you will regain the use of your factory fog lights and the switch! Only minor inconvenience is that the switch will always be hot, so you gotta be sure you shut your fogs off each time you're done with them. Nice thing is that the fogs are now always available, and they will not be affected if you hit the high beams. Be careful regarding on road legal issues with this, but this is a nice feature off road use. If you ever have to do a tech inspection, just remove the jumper and claim the fogs don't work.