Hi Nicholas,
I had forgotten to compare the trimmed file to the original file, and in fact, the primer were not trimmed.What a dumb mistake 
Both files have the exact same sequences, so the primers were in fact not removed.
I re-read the article by Taylor et al., 2016, who designed the primers and he states that, "forwards reads obtained from the Illumina sequencing are in reverse orientation w respect to ribosomal operons." So I have found the issue but I am unsure about how to fix it. I found this, which says that ITSxpress is not suitable for this type of data. Embedded in that post was this link to one of your github post, but to be honest, I am stumped on how to deal with this. Do you have any idea or suggestions of how I can work through this problem?
Sorry about all the questions, but no one in my lab has worked with this new primers, so I am unsure how to move forward and or have anyone in my lab that I can ask about the issue.