Whirleybird has a good point here, salt in the sand/ cement mixture. If there is salt present it will create efflorecence on a larger scale.
I would not recommend "drilling holes" to "vent the ceiling, this in itself does not make any sense to me and I can't image how this would resolve any problems with water retention.
To fix the problem you MUST repair where it originates from, this is the outside/ exterior of your roof.
jr, I know you said it has been painted with "specialised rubber paint", this is elastomeric paint. I would have to assume that the paint is not doing its job properly, or that it was never properly painted correctly. You can't paint under direct sunlight (it cures too fast), you can't just simply roll it on quick (this doesn't allow for a thick consistant coat), you can't walk on it too much right after its been painted (this is usually when problems occur to putting the second coat on, and again manufactures recommendation is ...I think...3-4 hours after the first coat).
Take a look yourself up on the roof, if you can and look very closely to the existing "rubberized" paint. Look for tiny bubbles in the paint or "hairline" cracks in the paint.
Your will be wasting your time and materials redoing the interior, without correcting the problem at its source.