Polycarbonate is hydroscopic and so can absorb moisture from the atmosphere and installations depend on ventilation to avoid saturated air in the cellular structure which will condense under appropriate conditions.There can be a tendency during the first few months for some condensation to appear but after a settling down period it will disappear again. If there are unfavorable conditions this may take a longer time. e.g . high moisture laden atmosphere ,large temperature differentials between inner and outer surfaces of the sheet ,low roof pitch ,poor ventilation ,North facing conservatory.

If you get a period of dry weather removing the sheet closures and tapes and letting dry air circulate within the sheet will speed things up.

If the moisture is a very fine misting of the inside surface it could be genuine condensation. If it is larger discrete droplets it is more likely to have occurred due to problems caused by installation.

If it is caused by problems at installation it could be

1. Damage to the tapes where moisture is getting in

2. The seals around the glazing bars/flashing not being water tight

3. Moisture that was let in during fitting that is now trapped.

Once you have identified and stopped the water ingress you need to give the polycarbonate time to dry out. Do NOT use a hairdryer or any other appliance to dry the polycarbonate as  you will damage the polycarbonate.

Opal polycarbonate is a good option if you think your roof will be prone to condensation as it is opaque.

More information is available on http://www.daylightsystems.com/roofing/polycarbonate/marlonfs/