A femtosecond laser with a 1 kHz repetition rate and two different polarization states was used to fabricate low-loss waveguides in fused silica. Investigations of chemically-mechanically polished waveguide regions using near-field scanning optical microscopy revealed the presence of modifications outside the glass regions directly exposed to a circularly polarized writing laser. These waveguides also exhibited refractive index contrast up to twice as large as that of waveguides written with linearly polarized radiation. The observed differences in refractive index were shown by Raman spectroscopy to correlate to an increased concentration of 3-member silicon-oxygen ring structures. We propose that the observed differences in material properties are due to the polarization dependence of photo-ionization rates in fused silica.