Dude, I do not see where your confusion/problem is.
1) If you have taken 5.5 years to get a masters degree it just means you have done credits that cover both bachelors and master level.
2) I mention PhD because for transferability factors the maximum you can get is 50 points, making 2 or more, masters and PhD all the same.
3) No one said 2 bachelor's degrees are not eligible. All I said is that one can have their masters degree evaluated on its own and get maximum points.
"Highest level of education
(2) Points are to be assigned under subsection (1) for the highest level of education obtained."
http://www.cic.gc.ca/english/department/mi/express-entry.asp
After all is said and done the ministerial instruction has the final say.
Regards