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Manual Transmission acting funny in Neutral?

Has anyone heard of something like this: My 2004 Pontiac Vibe (i.e. Toyota Matrix) Manual 5-speed developed a bearing problem in the transmission. I know, because I just paid to have the bearing replaced.

Not 10 minutes from the shop, stuck in evening rush hour traffic, I notice that the car seems to be running rough, but only when the clutch is pushed in or the transmission is in neutral. Rough, like going over the washboard edge markers. And it was only apparent below about 20 mph.

So, I thought, maybe just the new clutch “working in”. I thought that for about 5 minutes, until the ‘Check Engine’ light came on…

Of course, the transmission guys need to look at it. But what could it be? And I’m not even sure it is safe to drive on now.


The first thing I would do is pop the hood and look around for a vacuum hose that got left off. If you don’t find that start looking for ones that might be cracked or split. This would cause rough running and the engine light.

If I didn’t find it I would close the hood and take it back. About 2 minutes with a code reader and they should be able to see what it is - and its probably some mistake with or injury to the vacuum lines.

And why would a missing vacuum hose cause an apparent roughness only in neutral?

Most of my reasoning was based on 3 things: 1) always just look for simple stuff first; 2) in order to mess with the transmission a lot stuff probably had to get disconnected, and it is easy to miss something like a vacuum line; 3) you said with the clutch in or in neutral, which actually sounds to me like it is mostly when you are stopped. A minor rough running condition could be not noticed while moving along rather than being at idle - so it isn’t necessarily about being in neutral - maybe.

And… under there somewhere was a 4th - you said when the clutch is pushed in - or in neutral - I was thinking along the lines that it is probably a hydraulic clutch, it may be tied into the brake system and be squirreling with the vacuum booster in some way.

I also said it is what I would do, so maybe its not what you would so - was the incredibly simple, cheap, 5 minute suggestion somehow annoying?

Have I run into you on the D.I. support boards, btw? Or is the screen name a coincidence?

I agree with Admitted. I think something was not hooked up right when the transmission was reinstalled. The check engine light being on means the computer has now recognized it. Call the trans place, tell them what happened, and ask that they send a tow truck. They will look it over, read the codes, and will tell you more of what is wrong. With the check engine light on, the computer knows what it is, so I’m not going to guess, either.