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According to http://blog.stackoverflow.com/2010/07/new-per-site-metas/ and How does the reputation on parent and on meta site work?

Reputation is always inherited from the parent site.

However it is not obvious from the meta site UI.

It causes people's confusion, e.g. see

Issue with reputation

Upvoted question having no effect on rep in Code-Review meta

How does reputation between the main site and its meta work on SE 2.0?

It was strange for me to see that someone has a big reputation on meta site, when he has only one or two questions/answers and it took me time to find the reason.

It will be good to improve UI on meta sites

  1. Change tooltip on user info from "Reputation score" to "Reputation score on parent site"

  2. On user profile page change "Reputation" to "Reputation(on parent site)". It may be required to change position of badges on profile page to highlight that that badges are earned separately on the meta site.

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4  
I don't know how often people use the tooltip, but I don't think it's very often, so I don't know how this would solve the issue. –  Emracool May 5 '13 at 2:25
    
The reputation tab in your profile for per-site metas is missing. I think that should be explanation enough –  hjpotter92 May 5 '13 at 3:01
    
@hjpotter92, it is obvious, if you already know the rule. Absence of some menu doesn't explain anything. –  Michael Freidgeim May 5 '13 at 3:44
    
It's explained in the meta FAQs though e.g. here. (Not saying this can't be improved, but it's just one click away already.) –  Mat May 5 '13 at 4:16
    
@mat, Not everyone starting use the site from reading FAQ :) –  Michael Freidgeim May 5 '13 at 4:30
    
I know, but that's kind of exactly the place where you should go when you don't understand something. –  Mat May 5 '13 at 4:35
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