I'm trying to embed Type3 fonts generated by Scribus. In the preflight fix, it changes the text to glyphs

I'm trying to create a PDF where all the fonts are embedded. I have fonts that are name Fo1S0, Fo2S0, etc. that are generated by Scribus (the open source layout program that I used...) and when I run the preflight fix to embed all fonts, it turns them to glyphs.  In the document itself, I only use Times New Roman and Arial. Not sure why on only certain pages those fonts aren't recognized and are turned into the Fo1S0 fonts.  Is there any work-around in Adobe that will not turn them into glyphs and just embed them as the Times New Roman fonts that they really are?