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Hey Goobatastic, the problem you have is very simple to resolve.
What you did was, while sculpting you had material channel turned on ( m button wright next to the zadd and zsub) and what happens is that you paint the currently selected shader directly on to your model while you sculpt.
Anyway to solve this simply make sure that you have that m button turned on (highlighted in orange) select the flat color shader and go up in the color section and press fill object and that’s it.After that you select back the material you wan’t and continue working.Just make sure to turn of the m button after when you go back to sculpting.
enjoy
Thank you very much ja-popov you are a life saver. 
Does that mean i can carry over the shader information on the texture map?
Yes and no. Your texture can contain embedded materials, which is really an index of which material slot is used for which part of the texture. However, that info will generally only be meaningful in ZBrush. If you check out the Texturing part of ZBC’s FAQ you’ll find some topics on this subject.