The prosaic description you've presented is insufficient for us to provide any concrete help; what we really need is a SSCCE.

There are many ways colours may be initially specified. See Tk::options for items listed under STANDARD OPTIONS at the start of TableMatrix, and the remainder of that documentation for other options. There are also a variety of ways you may query and change colours: search for names that are, or include, cget and configure in both of those documents. Your post does not contain information about how you've used any of these.

We also have no idea about your cell data: hard-coded text; text derived from some expression; embedded windows; or something else. This may be relevant to your problem but it's impossible to say at this point.

Please keep your SSCCE short and to the point. A table consisting of a 3x3 matrix is probably sufficient. Your issue revolves around colours; we don't need to see options such as -bd, -relief, -ipady, -anchor, and so on. Your SSCCE needs to be runnable code that reproduces your problem; it must include the strict and warnings pragmata.

It is often the case that writing an SSCCE that focusses on a specific problem will actually highlight the issue and present a solution. However, if that's not the case, the information requested should be sufficient for someone here to help you.