I've been looking at the "buy menu" encyclopedia icon and the png file:
I think what's happening is this:
My compression routine starts out correctly enciphering transparent areas of the SHP images (notice how the hull is mostly good?) and then somewhere things break.
I think what's happening is something causes the pixel variable being scanned to hang in memory and refuse to be updated; explaining how the hull on the first image works mostly fine, then the turret is flashing transparent.
Either that; or the true color to indexed color flattening code is bugging out somewhere; reading index 255 as a different index (one that happens to flash)
EDIT:
And I think the reason why other zoom levels work; but not the "Default" is because your zoom and rotate routines use interpolation.
So my program is probably outputting transparent pixels as something like index 254 or something (which is a known flashing color index); so it flashes in "normal" view.
But when you zoom in; the interpolation code moves it into pixel value 255; and it becomes transparent again.