Do you happen to have a copy of the/a problem PDF that can be shared? I’m wondering if I can reproduce the problem.
It’s very likely to be Ghostscript that’s the “interesting” piece here, not ImageMagick. For PDF reading ImageMagick more or less just runs Ghostscript on the command line.
One thing to keep in mind if you’re trying to use a different Ghostscript for ImageMagick: if you’re installing it to a nonstandard path like /usr/local/bin or under /opt you may need to update ImageMagick’s delegates.xml file to force it to use the “good” Ghostscript by, for example, updating calls to gs to /usr/local/bin/gs. Making sure the appropriate folder is first in the PATH environment variable also probaly works fine but that can be annoying to set in the web context sometimes.