I think the problem could be the way the default color is changed by the colorscheme. I've looked at some colorschemes that set default merely by:
set background=light
or
set background=dark
Not sure what limitations of those are. I don't think those work in terminals.
In any case, you should be able to manually set background in a terminal by using the 'Normal' highlight. Insert it into a spot before most of the 'hi' commands in the colorscheme file and it should provide defaults they will work with. For example:
hi Normal ctermbg=White ctermfg=Black guifg=Black guibg=White
Change ctermfg (color terminal foreground) and ctermbg (color terminal background) to be whatever you want (or whatever color you were expecting to see in the colorscheme but now aren't seeing). (Remember, though, if the colorscheme already has a setting for hi Normal then this probably isn't your problem.)
For ctermbg and ctermfg you can enter color names, but I think there is only a fairly limited number:
Black
DarkBlue
DarkGreen
DarkCyan
DarkRed
DarkMagenta
Brown, DarkYellow
LightGray, LightGrey, Gray, Grey
DarkGray, DarkGrey
Blue, LightBlue
Green, LightGreen
Cyan, LightCyan
Red, LightRed
Magenta, LightMagenta
Yellow, LightYellow
White
Otherwise you should be able to use a number from 0 to 255 in place of the color name. Or this script gives rough idea, and lets you see how you could also set up to use more color names:
Vim script with color settings
Also, there are a number of scripts that help you use or convert colorschemes written for gui for use with cterm. E.g.,:
Colorscheme support for cterm
Does the overall settings for the terminal window have something to do with it?
Maybe, but I'm pretty sure a properly written Vim colorscheme will override any terminal settings you've made. At least they do for me in Windows and on Ubuntu. . .