Misfire on Idle Only/Mk6 GTI help

[DONO]

Hi Everyone, first time poster here.

My partner bought a mk6 Golf GTI a few months ago and we both love it, so much so I'm considering getting a Mk6 R, however we've run into an issue.

A few weeks ago it has developed a misfire on cylinder 2 confirmed by mechanics, (however they refused to work on European cars, aussie mechanics can be crap), I also bought a OBD2 reader and it says generic misfire for cyl 2 as well.

When we turn the car on it idles rough.
It ONLY happens on idle, even a little throttle and the issue seems to disappear and it seems to run smooth, driving it around and it causes no problems until the car comes to a stop after a few seconds. If it occurs (and I can hear and feel it running on 3 cylinders) I am able to turn the car off, and when I turn it back on straight away, it doesn't immediately come back unless I idle for about 30sec.

**I have replaced the spark plugs,
**Compression tests showed good across the board,
**I swapped cylinder 1 and 2's coil packs and it still shows misfire for cyl 2 only (to isolate any causes),
**I took the manifold off and replaced the injector for cyl 2 and put it all back together, still no luck. (Also anyone have suggestions for removing the carbon buildup other than blasting it with walnuts or whatever?)

**--UPDATE/EDITED 1--**:
*I have since replaced the PCV Valve and hoses with no help on fixing the issue.
*I have done a home-made smoke test on the intake system (unplugged a PCV valve pipe from the manifold and connected hose and smoke to it) and found no leaks (smoke only comes back out the intake)

*I have just been offered a new job requiring me to relocate, so I only have about 3 weeks to get it sorted. I will attempt to book it into a local VW specialist to get it sorted as I do not have enough time left to half-do the job unless its something easy. I will again update this thread when I have more answers on what the cause of the issue is.

Does anyone have anything to add to this or can suggest if it would be likely caused by something else? I have a fair bit of experience with cars (mainly jap) and nothing else sticks out as obvious to me so far, but any suggestions are welcome.
*I will also update this thread if I find the fix regardless.

[Nino]

Welcome to the Forum and good choice of car!

Ok, this is how I would tackle it.....

1. Vacuum / Air Leaks (very common on TSI engines)
At idle, the ECU relies heavily on vacuum readings. Even a small vacuum leak can cause a lean misfire on one cylinder.
Since it’s isolated to cyl 2, it could be:
- Intake manifold gasket around cyl 2.
- Injector seat/seal not sealing perfectly.
-A hairline crack in the intake runner near cyl 2.

Check: Spray brake cleaner/carb cleaner or use propane around the intake area near cyl 2 while idling. If the idle changes, you’ve found a leak. Smoke testing the intake system is the best method.

2. PCV Valve / Breather System
You’re right to suspect this they’re notorious on these cars. A failed PCV can cause unstable idle and lean misfires.
The dipstick test isn’t always conclusive. A failing diaphragm may act up only under certain conditions.

Check: Pull the oil cap at idle if it hisses strongly or the idle drastically changes, the PCV is bad. Honestly, for the cost, replacing it is worth it as preventative maintenance.

3. Carbon Buildup on Intake Valves
Direct-injected engines like the EA888 are notorious for carbon buildup. Even if compression is good, sticky valves can cause poor air/fuel mixing at low airflows. Walnut blasting is the gold standard, but if you want DIY alternatives:
- Intake valve cleaning sprays (not as effective but can help).
- Manual scrubbing with brushes/picks when manifold is off.

If cyl 2 valves are more coked up than the others, it would explain a misfire only on that cylinder.

4. Fuel Rail / Wiring / ECU Driver
Less common, but worth mentioning since you swapped injectors: The wiring harness to injector 2 could have an intermittent fault. The ECU’s injector driver (rare, but possible) could be weak on cyl 2.

Check: Swap injectors again but also swap the wiring connectors between cylinders (with adapters if needed) if the misfire moves, it’s wiring/ECU, not the injector itself.

Also do a continuity test on the wiring from injector plug to ECU.

5. Camshaft / Timing / Valvetrain
Since it clears up with throttle, it’s less likely, but sometimes worn cam lobes or lifters can cause low-speed misfires.
Would typically show as uneven compression or ticking, but since you say compression is fine, this is lower on the list. OR if you have the chain engine (If you have the R or the Edition 35, its belt not chain) you could have "chain strech" or worn chain guides.

Have a watch of this video
https://youtu.be/L5EvMjoeMvU?si=h4lA7o7qgPjItM3e


I had the same issue on my R32 years ago, I changed all 6 plugs, all 6 coil packs and in the end, it was a split in a vac hose

[DONO]

Thank you Nino, your suggestions have been a great help!
Another question in conjunction to vacuum lines, im guessing not all of them will directly be tied to the same airflow/passage as the intake? and if not is there an easy-ish way to test them?

Update 1:
*I have since replaced the PCV Valve and hoses with no help on fixing the issue.
*I have done a home-made smoke test on the intake system (unplugged a PCV valve pipe from the manifold and connected hose and smoke to it) and found no leaks (smoke only comes back out the intake)

*I have just been offered a new job requiring me to relocate, so I only have about 3 weeks to get it sorted. I will attempt to book it into a local VW specialist to get it sorted as I do not have enough time left to half-do the job unless its something easy. I will again update this thread when I have more answers on what the cause of the issue is.

[Nino]

Good update mate, thanks for sharing. Since you’ve already swapped the injector, coils, plugs, done compression, replaced the PCV and even smoke tested the intake, that rules out a lot of the usual suspects.

Vacuum leaks in general would affect all cylinders if they’re on shared lines (brake booster, evap, etc.), so the fact it’s only cyl 2 makes me think it’s either something local to that runner or valves. An intake manifold gasket leak on cyl 2, sticky/built-up intake valves, or the runner flap system being jammed are all pretty common on these engines.

Another thing worth checking is the injector wiring. Sometimes a poor connection only shows at idle when the duty cycle is tiny. A specialist can do a current ramp test or continuity test on that harness to be sure.

If you’ve got a chance to pull the manifold again, have a look down the ports at cyl 2 if it’s much dirtier than the others that’ll pretty much confirm carbon buildup, which is a classic idle-only misfire cause. Walnut blasting is the only real fix there.

Given your timeline, I reckon you’re on the right track booking it in with a VW shop. I’d ask them to specifically check:

- Intake valve carbon buildup
- Runner flap operation
- Injector wiring and ECU driver

If I had to guess, I’d put money on cyl 2 valves being coked up, with the runner flap issue being second most likely.