Yeah, there shouldn't be any water left in the sample tube/filter after it clears it out.
I have my filter halfway up the sample line, out of the water and held vertically. I found that when I first set it up the filter was at an angle and so was trapping some air.
The system seems quite sensitive in terms the volume coming through (which I guess relates to how these titration measurements work...). With 8' of sample tube that will be magnified for you.
When I was getting weird readings early on it was because my sample tube had shifted and it was getting air trapped in sections. Having said that, since if gotten it all set up properly it has been very solid. So it is worth the time to fiddle with the physical setup and then make sure its secure.
Cheers, Tony