The chances are the bitmaps for the custom skin where not saved in the correct format.
Keeping old dsystem folders around is never a good idea, they often conflict with later updates. Better to let the xmenu.dat file autogenerate a new dsystem folder and put the correct saved bitmaps in there.
Using older firmware is of course, your prerogative but it is the major cause of errors with newly released roms and the first thing anyone will suggest you do is update.
The newest firmwares do NOT default to the 3D menu, they removed it entirely due to it being a memory hog and rather clunky. Only the 2D menu is possible.
The text colour can be changed via the settings under [msg color] in the global ini. There are three entries, one for red, one for green and one for blue. They are additive and range from 0 to 31. All three set to 31 results in white text, all set to 0 results in black. The text colour is the same for BOTH screens, you cannot have different text colous for the top screen and the bottom.
You CANNOT change the highlight colour, at least not via the global.ini. It is a hard coded 'invert highlight. Anything in your desktop.bmp that falls under the menu area will be inverted as a highlight (thus my preference for grey which is easier to manage).
Changing the scroll bar colour is also difficult and often unresponsive to entries in the global.ini you can make it nearly transparent but not completely, solid colours are possible but usually look terrible.
You can make the bars that appear at top and bottom of the lower screen by default, transparent.
You cannot turn off the firmware version number that appears at top right and it will ALWAYS be snot green coloured.
It is in general a terrible menu to skin and will remain so forever...