I used to have a similar problem when trying to publish my BPEL process,
although the error message I got only said 'NullPointerException'. Anyway,
the problem occured because the WSDL-defintions that I used for my partner
links used the <import>-tag which obviously creats some trouble in the
bpel designer at the moment.
I imported the needed WSDL-definitions into the project and edited out
(deleted) all <import>-tags. After that I had no more problems
publishing...
If that is an option for you, give it a try. It might be due to the same
reason.