This issue appears for me on an iPad 2 iOS 5.0.1 using:
/api-3/6/14/main.js
/api-3/7/15/main.js
/api-3/8/7/main.js   (The latest)

Could this be the same as this issue?
https://code.google.com/p/gmaps-api-issues/issues/detail?id=3373

It is the same issue - but it was fixed a while back.

Then, in iOS 5, it became an issue again. 

Reproduced on an iPad.

We are running into the same issue, on both iOS 5.x and 6.0 beta, using the latest maps api. This issue makes embedded maps unusable on the ipad and iphone if they are part of a scrolling page. It's not only the pinch/zoom which is affected; the Drawing Library tools are offset as well (but only if one drags to create a shape, just tapping to create points works fine). Has there been any progress, or a workaround?

Fixed in 3.9 and 3.10

Great, thank you!

This still occurs in v3.9 as for today. Besides that, when people zoom on a page by pinching and this zoom is a little bit off, the setCenter and setBounds functions also show the same deviation. The more these functions are used, the more the positions on the map change. 

This can be confirmed by using the following Google provided example page: https://google-developers.appspot.com/maps/documentation/javascript/examples/directions-complex
When randomly zooming and pinching (zooming in and out some time - from the corners, not from the center of the map) and then asking for directions, the setBounds puts you at a completely different place than where the route actually is presented on the map. I think this is all related to this issue, although the effect sometimes is hard to reproduce when only pinching from the center of the map. On first initialization and without pinching, the setCenter and setBounds keep giving the right values.

It actually bugs me very much as I thought this problem would have been solved since the 10th of September. I am producing a mobile webapplication which will be used by more than 200.000 people within two weeks, so this definitely makes the webapp pretty unusable.

This is tested and confirmed on the following devices:
iPhone 4S w/ iOS 5.1.1 / iOS 6.0 (although effect is less visible because of screen resolution, only after following the above procedure for a while)
iPad 1 w/ iOS 4.2.1
iPad 2 w/ iOS 5.1.1

The issue is still there when map is loaded in a friendly iframe