May I suggest re-reading the basics of repaint-kits regarding the various file formats one uses. I fail to see what your current problem has to do with Pixia. It looks to me like a misunderstanding of file formats and which ones to use where.
There are several tutorials online -- including here at SimV. May I suggest
reading this one again.
P.S. Save the finished repaint out of Pixia as a 24bit.BMP file (this is the default as I recall); those of us using Photoshop can save as 32bit.BMP for higher detail (and use directly in Fs9, in select cases).
Disclaimer: "Please Note: there are many ways to repaint these planes - I'm describing the one I use, which may not be the "best", but works well for me. "