I saw a similar problem in 16.04 with PDFs being opened with ImageMagick. Trying to open With Document Viewer and set that as the default made no change. I saw in mimeapps.list that there was both an image/pdf and an applications/pdf entry. I removed the image/pdf entry that pointed to ImageMagick, and left the very last entry in the file, which was the applications/pdf entry with Evince.
I saw a similar problem in 16.04 with PDFs being opened with ImageMagick. Trying to open With Document Viewer and set that as the default made no change. I saw in mimeapps.list that there was both an image/pdf and an applications/pdf entry. I removed the image/pdf entry that pointed to ImageMagick, and left the very last entry in the file, which was the applications/pdf entry with Evince.