I have identified the problem; it does not always save as Patch, but as the type it was loaded as.
Although it is pretty relevant, I don't think it justifies a new PFM build.
I wrote a little tool to change the pack type of a given file so you can switch after saving, added to OP.
You'll have to call it from the command line, like this:
Valid <packtype>s are (b)oot, (r)elease, (p)atch, (m)od, mo(v)ie.
setPackType.exe <packtype> [packfiles]
Make sure the files in the parameter list are packfiles; you'll probably break other files.