In case someone else finds this thread when Googling, like I did:
I had what appeared to be the same problem for a while, and after some digging I noticed that the R.java file got correctly built, but was ignored for only one of my source files. The problem for this particular file was that Eclipse had "helpfully" added the following line at the top:
import android.R;
That effectively hides the project R stuff. Just remove it and everything will be fine again...