Measurements of the circular polarization of Balmer-u radiation emitted by excited hydrogen atoms, following the transmission of (20 -50)-keV protons through thin, tilted amorphous carbon foils, exhibit markedly unexpected behavior as a function of exposure of the foil to the proton beam. Specifically, the circular polarization changes from an initially well understood tilt-angle dependence to a behavior which, for low tilt angles, gives the opposite handedness of circular polarization from that predicted. In addition, the degree of alignment, indicated by the linear Stokes parameter MII, is enhanced also as a function of dose. These changes in the tilt-angle dependence of the Stokes parameters have been systematically correlated with beam-induced graphitization of the foil, which is observed to occur from Raman measurements.PACS number(s): 34.50.Fa, 78.30.j, 13.88.+e