I have the same paint installed. The way I fixed the helmet was by renaming the file. Remove the "bmp" from the end extension and replace it with "dds". The file should already be saved as a .dds format. You might need to open the .lua file, and see if the line of code with the helmet filename is also spelled correctly. In fact I'd check this first to make sure that it's not actually written as something else. You can always just change the name in the list to match what you have for your helmet name.
make sure it looks like this:
{"pilot_F5E3_helmet", 0, "pilot_f-5e3_helmet", false};