I have had my 2005 Passat between a trusted mechanic and the dealership for the past several months and they cannot seem to solve my problem so I bring it to you!
When I start it in the morning it starts well yet runs very roughly for about 30 seconds to a minute (lately this may even happen after sitting a few hours and not just over night and the CEL light will flash) during this time however I have never had it stall and I do not need to give it gas, I just have to wait a bit for it to smooth out. Also, i have a vibration that occurs at various times, usually while idling at a stop light for example, it is in the driver side area and ranges from a mild hum to a door shaking, teeth jarring, rumble strip like problem.
Before you suggest all sorts of normal things the mechanic and dealer always say there is a “misfire” and they have replaced everything from spark plug wires to PCV valve to battery and other things too . .
So . . any ideas??
Also, this seems significant . .it is considerably worse when I park downhill for a bit such as at my parents house or my new job . .hence the recent exacerbation?
I am understandably tired of going and having various parts replaced for a range of $100 - $200 and the CEL light turned off, and it seems to run well for anywhere from an hour or so to a couple days … and then it all starts again . . .at times I just ignore it cuz this is so silly! 
But maybe I am doing damage or maybe I could finally get an answer . .you tell me!
Bad or clogged fuel injectors could cause similar problems. Cheap fix try, sea foam and a new fuel filter.
That CEL (check engine light) is just a kid in class waving her hand trying to get you attention because she has the answer. You need to have the codes read. Some places will read them for FREE. Try Autozone or Advanced Auto Parts. Get the exact code (like P0123) not just their translation into English and post it back here.
I am having the exact same problems!! 2005 Passat wagon. When I brake and stop it will “sporadically” start missing-out and run rough. The engine light will blink and after 30 sec to a minute it will smooth out and run fine. The thing about the hill is what is driving me crazy, as it seems to perpetuate the problem, as well does sudden, more abrupt breaking.
1st - I pulled the codes and show a (P0301 Cylinder 1 Misfire and P0302 Cylinder 2 Misfire). I pulled and replaced all four plugs and replaced the ignition coils on cylinder 1 and 2. Cleared the codes from the ECM (engine control module).
2nd - I added Chevron Techron to the tank to clean the fuel injectors. Running BP premium fuel.
Still no change, still throwing the same codes.
I think I’m going to try replacing the mass air flow sensor to see if that will make a difference.
If this problem has been resolved please let me know what it was!!
If you haven’t had the coil packs on the plugs replaced, that would be the first place to check. My 2004 just had the recall work for those done this last weekend, just after it started doing exactly what you’re describing. They’re a known weak point.
Maybe someone should have considered the loss of residual fuel pressure when the car has been sitting. Fuel injection systems are designed to hold a certain amount of fuel pressure in the lines while the car is not running. This allows the engine to start instantly later on.
If there is a leak in the system the residual pressure will be lost and the engine will run poorly for a short time after a startup. This is due to air in the lines being purged by fuel pressure.
Ever seen a garden hose spit and sputter after lying out in the sun for a while? Same thing; it’s the air being purged out of the hose.
Pressure loss can be due to a leaking injector, leaking fuel pressure regulator, or the most common cause of all, a faulty check valve on the fuel pump.
This can be easily tested with a fuel pressure gauge.
The erratic vibration could be a separate issue. Get some place like AutoZone, Checkers, etc. to run a quick scan (it’s free) and see if anything pops up there.
On this problem there is just not enough known to make much of a guess short of throwing something out there about an Idle Air Control valve problem or possibly a fuel pump that is acting up erratically and causing an engine performance problem.
Hope some of that helps.
Well, after replacing the coils on the 1 and 2 spark plugs as well as all four plugs (gapped to specification), replacing air filter, and finally a new Mass Air Flow Sensor, my Passat is still doing the same thing. One thing I have noticed – when it starts missing I can rev the engine to 3000 rpm and it will smooth out. Might this be vacuum? The fact that it is relegated to cylinders 1 and 2 and not 3 and 4 leads me to discard the fuel pump theory.
Time to stop changing parts and start doing careful testing.
I would start with a compression test on the cold engine.
I had a similar problem with a 1990 Ford Aerostar with a 4.0 liter V-6 engine. The problem turned out to be coolant leaking into one of the cylinders. After the engine ran for a minute or so, the cylinder would clear itself and the spark plug would then fire normally. Your check engine light is coming on because the spark plug is misfiring on start up. In my case, the dealer replaced the head gasket which worked for a while, but the problem reoccured. It turned out that a cylinder head had a hairline crack. Fortunately, the van was under warranty and the entire engine was replaced. There is a test for a bad head gasket. This might be your next step
I have a 2002 Passat with the exact same symptoms as your 2005. I have had it in multiple times for the CEL flashing with the same results as yours. Did you find a solution to the problem?