I’m just shooting in the dark here, but what i think is going on is your menu “thinks” its on the blog page when its really on the “CPT” page? is that about right? if so then you need to select a blog page in the admin section. Under the Settings menu click on the “Reading” sub menu. There you will find two select boxes. I’d suggest you select a specific page for your home page and your blog page. see if that corrects the issue.
I’m not even in the right ball park, please let me know.