update: this issue is connected with Chrome's text zoom feature - see the bottom of this post.
I quite often see this sort of thing:
Sometimes when I reload the page, the equations will go back to being centred where they should be - but sometimes not. This is with Google Chrome (31.0.1650.57, though it's been an issue for a while) under OS X 10.8.5.
This is with the Math renderer set to "SVG", because I like my equations to be pretty.
The problem is not specific to multiline equations. Here is an example with a single-line one, albeit a rather long one:
It seems not to happen with all equations, but I'm not sure what the pattern is. I'd say it occurs with more than 50% of them though.
I habitually browse with Chrome's zoom level set to one or two, because my eyesight is quite poor. This problem doesn't occur with the zoom set to the default level, and it also immediately disappears if I change the zoom level, so as a workaround I can quickly change the zoom to something else and back again (
+ on my Mac) to get the correct formatting.