Surface enhanced resonance Raman scattering (SERRS) has been applied to investigate defects in purified and carboxylated single-walled carbon nanotubes (SWCNTs). For both samples SERRS spectra with temporal fluctuating peak intensities and positions in the range of 1000 to 1350 cm-1 have been observed. A series of peaks in this window were observed to coincide with peak positions that have been assigned to arise from Stone-Thrower-Wales and heptagonal-pentagonal intramolecular junction defects on the nanotubes surface. Two possible origins for these fluctuating spectral features are discussed ie the presence of Stone-Thrower-Wales defects in SWCNTs or amorphous carbon impurities.