WPML Broken

The domain mapping plugin used to work with the WPML SEO setting "Different languages in directories" but it is now incompatible. WPML only works in "Language Name Added as a Parameter" mode. When I try to try to save the languages in directories setting (Language Configuration Page) it spits back the following debug information:

It looks like languages per directories will not function.

This can be a result of {edit: a bunch of things it isn't}

_How to fix_
When WPML accesses http://{edit:thecustomdomain}/{edit:lang}/?___icl_validate_domain=1 it gets:
<!--http://{edit:theblogsubdomain}.{edit:thesitedomain}-->
The expected value is
<!--http://{edit:thecustomdomain}-->

Not sure how to make the domain "validate" like it used to...
All help appreciated,
Thanks,
A