i've never heard of this, have you tried reflashing your current version of cyanogenmod? or the base ROM required for it and then flashing your version of cyanogenmod?
i had a problem where i flashed a version of cyanogenmod and it didn't show me the google login, or have market place at all. after reading the wiki it gave me a rom to download and flash before flashing cyanogen but you said you had the market to begin with so i have no idea what-so-ever...
as for just using that marketplace and the other just "disappearing" i've never heard of anything like that.

i've used it once or twice, but it never affected anything else.... um also, i'm not sure about this, but im sure you can unzip a rom with market on it, install it using adb directly as see if that works?