hgrc - [defaults] does not apply ignore (-X) to listed files
create a file called test.txt in your repo and add the following to hgrc:
[defaults] status = -X test.txt commit = -X test.txt
Although the command-line ensures that test.txt is ignored upon hg status and hg commit, when you view your working directory in thg, it still sees test.txt as dirty and it also commits the file if you choose to commit.
Ideally thg would follow the same convention as the command-line, though perhaps a message should go to the console that states the file is being ignored during the current operation (status or commit)