If you perform white tube cleaning on that line only, does it actually flush out?
I would figure there would be a clog in the waste line, or something else going on at the capping station, and even though the white ink retrieves, you shouldn't be left with a clear line after the maintenance fluid attempts to go through it (when you retrieve there is usually a residue left on the tube membranes leaving a hazing of sorts, as the cleaning solution and air is pushed through the line, it should turn clear).
You may also want to check your waste hose. When my printer was installed the tube/hose went all the way to the bottom of the waste jug, the problem with this is it may not be able to pump out the waste ink and could clog causing all sorts of issues. I received a call from a Brother rep asking me to check that as I guess they were having issues with it. I had a fairly large buildup at one point in my tube as well as having that tube go all the way to the bottom, cleaned out the clog and trimmed it a bit.