Thanks for your reply
I do have a slight mismatch from what is dynamically added as the appID (com.domain.Appname) within the iOS publish settings panel and what is on the provisioning portal
Am I correct in thinking that I shouldn't be including the apple seed prefix in the iOS publish settings panel?
OK, I've managed to get this working. Unfortunately I can't pinpoint the exact reason it wasn't working but I ended up:
Removing all provisioning profiles from iTunes and the iPad.
Revolking both Developer and Distribution certificates in the Dev Centre and then re-issuing them. (followed instructions on lynda.com Bill W)
Downloading both certificates and installing into the KeyChain.
Creating new provisioning profiles for development and adhoc distribution, ensuring all devices have been added to it, download and install to iTunes and sync with iPad.
Create a new p.12 certificate using the new developer certificate. (followed instructions on lynda.com Todd Perkins)
Set the iOS publishing settings in Flash to use the new p.12 cert and adhoc provisioning profile.
Publish the ipa file.
Drag the ipa file into iTunes
Sync the iPad.
If you don't get the alert you've struck GOLD!
Relief!!! Going for long lie down now!