Dingemap, are you really loosing material on the column or did your peaks get broader with a resulting deterioration of the integration? If this was the case you may have the same problem that I have with a TSKgel Super SW 3000 (I posted on this, talked extensively to the manufacturer: no solution yet). After using TFA (or higher perfluoros) the peaks broadened badly, partially irreversible. I don´t know whether acidity or other factors caused this. Having been partially recoverable indicates that stripping via pH can not be the sole reason for the observation. It could be instructive to hear more about your conditions.
(The partial improvement after the use of TFA came about by "keeping the protein happy and solvated" with phosphate buffered saline [PBS] as mobile phase as well as protein solvent, and apparently by washing something off the column. Incidentally, keeping the protin well solvated can be an alternative to Tom´s "loading" with a protein.)