Drupal PHP filter being overwritten in Lexicon Module
I have been able to get a fix - but not an ideal one. I moved the PHP text format to be displayed as a first priority at admin/config/content/formats. Doing this preserves the PHP code after hitting save. The reason I say it's not ideal is because now PHP code will be displayed as the default format for making new pieces of content - fine for me, but I'm sure the client will wish they could get their WYSIWYG right away.

If anyone knows a way to target the display order of text formats for just one specific module, I'm sure that would be the solution.