It could be a leak in the normal feed line causing air to enter fuel. That leak is bypassed when switching lines.

But algae could have been introduced to your tank from a fuel station tank. I wouldn't completely rule it out but at the moment I'm not convinced that is the problem. A simple check would be to pump the tank dry using the method I described and then remove the strainer and see what it looks like. Or pump it dry and stick an inspection camera down the fill pipe and see if you can get a look at the strainer.

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1977 300d 70k--sold 08
1985 300TD 185k+
1984 307d 126k--sold 8/03
1985 409d 65k--sold 06
1984 300SD 315k--daughter's car
1979 300SD 122k--sold 2/11
1999 Fuso FG Expedition Camper
1993 GMC Sierra 6.5 TD 4x4
1982 Bluebird Wanderlodge CAT 3208--Sold 2/13