Took the roof down whilst changing out the door speakers for new updated ones. Once completed the roof refused to close at all and just got the audible bleeps as previously. Closed the roof manually and latched the boot in place temporarily as the full latching sequence of the upper boot can only be achieved when driven electrically. Went on a 20 minute drive down the local motorway, pulled over and tried the closing sequence and voila it worked.
This proves that in both instances the problem seems to be with my battery! even though the car starts first time every time there must be something monitoring the battery and telling the ECU that it doesn't have enough power, which a short drive to charge the battery seems to cure.
Not sure if this will help anyone but thought I'd post anyway as its definately a cause of the roof not opening or closing.