I suspect it is nozzle temp is too cold for the underextruded layers. Leave the printer in the TUNE menu while printing and monitor the temp closely when going over the problem layers. Consider increasing the nozzle temp a bit if thats the problem. There maybe some temperature isulation factor between the temp sensor or the heater and the block causing the PID controller to oscillate for the bottom/problem area.
Consider printing at anywhere up to 240C (240C is a safe temp for PLA but don't go any higher). The warmer you go the easier the plastic flows (less viscous).
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IRobertI 521
Perhaps you could try kicking the fans on more gradually if that's possible for your design. That way the head will have more time to compensate for the extra air flow. Since you say it coincides with the fans going up to full speed I'm guessing that the PID loop doesn't quite have time to react to keep the temperature stable.
You could also try printing a little bit hotter so that there's a larger temperature margin for the plastic to stay hot enough.
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