Poor flow and filtration are certainly contributing causes . . . and could lead to conditions in which you would tend to 'breed' highly chlorine resistant algae, since algae could retreat to low flow / low chlorine areas whenever you tried to attack the problem.

You still may have some very chlorine resistant algae. So, I'd still recommend the process above.

Also, in a situation like this taking borates to 50+ ppm is likely to help, if you want to pursue that.

Ben