I had a similar situation with an 1120-S I efiled recently, and I found a workaround. I'm not at my office so I'm writing this from memory. I think this is how I got it to work.

Create the Form 8936 as a PDF, then with the 1120-s return open, select E-File > Attach PDF Files.

Attach the PDF of the Form 8936, then select "Other" for the Type, then click on "Schedule and Description" and type an entry there. From the best of my memory, these steps allowed me to attach a nonbinary attachment as a PDF and efile the 1120-S successfully.

Good luck!