Sorry for the delay in responding to you - the reason for this is that we are currently undergoing a review of how we analyse hemispherical photos. Essentially, for all the reasons you mention above regarding 'optical centre', 'angular resolution' etc...and moreover the calibration process that is now required in CAN-EYE, we are moving to a different, freely downloadable software analysis program called Hemisfer (http://www.wsl.ch/dienstleistungen/produkte/software/hemisfer/download_EN) - the free version is fully functional (as well as far more intuitive than CAN-EYE), the only limitation being it's resolution limits. We are in the process of purchasing a number of licenses which give us access to the limit-free resolution version and can share this with you in time. In the meantime, may I suggest that you follow the link above and try running some of your photos through the free version to get accustomed to the software? For peace of mind, you can even compare some of the results from Hemisfer with CAN-EYE - we have also done this and there is good agreement (even with the free version). Let me know how you get on.
All best from Oxford,
Sam and the GEM team