In cases like this the first thing we usually suggest is that you upload your problem module to SCORM Cloud and test it there to see if it scores correctly.
As you have stated that your LMS is a custom job created for your company, it's possible that it's not truly SCORM compliant. If your module behaves consistently well in SCORM Cloud, I'd be blaming the problem on your LMS. If it also misbehaves in SCORM Cloud then you may have a glitch or some type of corruption in your module. In that case, try creating a small sample CPTX project with a single True/False quiz question and see if that will score correctly. If it does, your project may have become corrupted.