This can be due to a variety of factors, my guess would be either filementous bacteria in your floc causing float or overdosing the coagulant.
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There are several factors that influence settling. Here are some of them;
1. Rising sludge due to incomplete denitrification in the anoxic zone. The settled sludge in the clarifier enables denitrification if there are nitrates present (and some COD). The resultant formation of nitrogen gas lifts pockets of biomass to the surface.
2. Hydraulic overloading. Ideally the upflow velocity through the clarifier should be less than 1 meter per hour (and this is an upper limit, I would be comfortable with less than 0.5 m/hr). Variable incoming flow can play havoc with a clarifier if there is no flow balancing.
3. If the process is fully aerobic, you won't have any filamentous organisms and the biomass will comprise almost entirely pin point flocs. These settle reasonably well but a portion can also remain in suspension.
4. Do you measure the SVI? Ideally this should be less than 600 ml. If higher than 600 ml, you will need to remove some of your biomass.
You could find out more at http://hwt.co.za/sewage-treatment/hydrossis-process/