Thank you for your post and sorry that you have encountered a problem.
A support call has been created for you, the call reference number is F0059624.
Can you please enable the SQL Compare GUI logging? Right click the SQL Compare icon in the very top left hand corner of the GUI immediately above the file menu. ->Change the minimum logging level to verbose ->Recreate the error symptoms ->Repeating the right click the SQL Compare icon in the very top left hand corner of the GUI ->Locate the current log file.
Send an e-mail to email@example.com
with the above call reference number in the subject field of the e-mail and attach a copy of the log file to the e-mail.
Hopefully the log file will provide some information as to why you are experiencing the reported problem.