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As you've surmised, the reference line calculations are at a higher level of aggregation, so the average reference line is an average of the marks. For example, in the first column there are 8 marks evenly spaced from 4.5 to 8, so the average of those is 6.25 and that's where the reference line is.
To get an average from the underlying data can be tricky (based on the pills in your view), the simplest thing to do is to create a TOTAL(AVG([your measure])) calc, put that on the Level of Detail Shelf, and then add that as a reference line. If that doesn't work, then either the Compute Using setting needs to change or there's something else going on with how your data is set up. In that case, posting a packaged workbook (.twbx) with some sample or mock data would be helpful.
This forum post is one of several that goes into weighting reference lines: http://community.tableau.com/thread/110215