The bubblecount is a guide.. inserting the ph probe in the cr chamber is an accurate way of knowing your effluent ph is low enough to dissolve the media. 6.6 is a right value. But I guess somehow your co2 leak into the display. U have enough media in the reactive chamber?
Lowering the outflow might reduce the low ph prob, then u might have to recalibrate your co2 feed to the chamber too.