I just dove into it for a sanity check and the Pluto for Channels project does do the work to determine if a piece of content is a movie or a TV show. It writes out the <category>Movie</category> tag in its XMLTV output, which is standard.
I also checked a movie that's currently tagged that way, recorded it, and it showed up as a movie in the library.
So everything that can be done, is happening. If the item metadata doesn't have the appropriate information from Pluto, than this will fail, and there's not much Channels DVR Server can do about it. So it's possible some content is just tagged bad by Pluto.
If you're using another project to add Pluto as Custom Channels, then I can't speak on that, and it could possibly be the issue.
If anyone is using the aforementioned project, and can see a currently airing movie that isn't getting put into the library correctly, I'd be happy to inspect the data to look at it. Or if you want, you can too at another time if you run into this issue. Just check to see if the output of the XMLTV has the tag I mentioned up top.