Ah, it seems you have a good grip on this stuff. Very nice.
My best guess is that PSP has changed it's pal file format since MDMRE wrote his paletmaster program.
I suggest you use C-POD
http://mtm2.com/~mtmg/repaint/index.shtml
It really simplifys the whole repainting process as it convets RAW+ACT directly to bmp, then you get to edit the bmp, save as 256 colors, and it converts right back to RAW+ACT, no need to deal with pal files.
Plus phinny wrote that tremendously great tutorial that gives you ever single step.
If u need help ask here.