Sorry for the delay in replying back to you, it took longer than expected to create a test machine with two instances of SQL 2008 R2 and then apply SP1 and CU6 respectively.
Unfortunately I am still unable to replicate your reported fault symptoms.
So I can continue further with my investigations, would it be possible for you to generate a SQL Compare snapshot of both the source and target databases?
If the answer is yes, can you please attach the resulting *.snp files to an e-mail with the following call reference number in the subject field of the e-mail - F0059596. Please send the e-mail to email@example.com