Thank you for your forum post and sorry that you have encountered a problem.
When creating the deployment script, SQL Compare should create the database objects in the correct dependency order. However, there are situations where SQL Compare gets the dependency order incorrect.
A support call has been created for you, the call reference is 8009. Would it be possible for you to create a SQL Compare snapshot file of each data source?
Next send an e-mail to email@example.com
with the resulting snp files attached with your call reference number #8009 in the subject field of your e-mail.
Using the snapshot files, I can then attempt to recreate the problem you have reported.