Yes, this is exactly the problem I've been trying to communicate via their broken e-mail server and posts here - you've forgotten to add a bunch of files in the admin subdirectory.
You need to do a "cvs add *.xql" in that directory followed by a commit. We can then help you out.
As far as "unique" goes, no, you do not need to change the query in the .tcl file. The query dispatcher has replaced it with the proper PostgreSQL query, which - as can be seen from the log file you've posted - contains "distinct()". As to why it is failing now, as Jonathan says it will be a lot easier to help you after you get all your files checked in properly so we can install the package and take a look.
