Thanks,
I will give it a go when I have a bit of headspace. Actually the issue I describe and other describes is a bug in SNAP. I have described it but it has not been flagged as such. The ensemble of angles in Snap is exported as a zero-phase interferogram whereas SNAPHU expects a minimum-phase interferogram. It is a pretty big mistake and I am certain it has been in the software for a while as I have seen similar results to mine on several posts. Anyway, at the moment I script to correct this and it kind of works.
Cheers,