MD works, resides in VA

I haver been dealing with Maryland about a 2006 return. The cloient lives in VA and works in MD I did a 505 and 760. I was advised that there was no difference in treatment between W-2or 1099-Misc. She's an independent contractor. A schedule C was

done.  I was told that I needed to credit the income from Md to VA.  VA taxes created a zero balance and all that was left is a credit to MD of $3000.  3 years later Md is coming back and saying that if a Schedule C is done then Md needs to pick up the money.  That doesn't seem right. I need to contact the MD today. What do you suggest that I do?