I'm not quite sure what I'm looking at...
How are you pasting? Just ctrl-V?
Where are you pasting from? Within Companion or from some external source? If an external source, what happens if you use the import image dialog?
What about if you paste transparent? (ctrl-shift-v)? (actually no, that won't help...)
Also note that if you're pasting from another app, I believe the palette information is lost, so Companion has to re-map the RGB values of the pasted image to the view's palette.
(nice font, btw)
[edit:]
I suspect this is happening because I'm removing the current transparent color from the list of colors we can "map to". I'm not sure I should change that default behavior, otherwise folks will get random transparent parts in the images they paste in...
[edit:]
You can also "paste special" (ctrl-b), which will bring up the dialog that gives you more control. I think you can get this to work if you uncheck "Exclude from palette" in the transparency box. Yeah? (you'll need to uncheck it each time you invoke it, it doesn't remember the setting :-( )