Where are these supposedly mysteriously appearing rupees?

Solution 1:

My reading would suggest that the rupees appear during normal activities when you would already get rupees, such as cutting grass or killing enemies. You would just get more of them than normal.

http://www.ign.com/wikis/the-legend-of-zelda-skyward-sword/Rupee_Medal

I don't know of any hard numbers to support this, so it might not be an especially dramatic increase in rupees. It might become more noticable with more than one rupee medal, because anecdotal evidence would suggest that the effects of different medals stack. See this question: Do medal effects stack?