Herman, assuming you've reversed or swapped-out all the connectors (including headshell leads) as a diagnostic precaution, I would have to guess that since what you changed was the pre-preamplifier/preamplifier chain, you might have engendered a slight overload problem somewhere in the gain structure. Infrasonic info could then result in clipping distortion products yielding the 'scratching' sound you actually hear. Why this would manifest itself in only one channel is hard to say, but since you report that reversing the TT leads reverses the symptom, there could be a response imbalance within your cartridge which could be innocuous under other circumstances (such as with your gear before). I assume your subsonic filter was inserted after the VTL - if so, try inserting it after the step-up and see what happens (just keep your volume control turned down at first, as putting the filter before the preamplifier could add a lot of other noise).
Either that, or as you say, your cartridge is screwed up...Best of luck! :-)
Either that, or as you say, your cartridge is screwed up...Best of luck! :-)