Loss of bass in Audio research vsi 55

My set up:

Audio Research vsi 55 with Aurora Power cable
Harbeth Super HL5's with Nanotek Golden Strada speaker cables
Graham Slee ERA V Gold with Siletch interconnects
Thorens TD2010 with shure cartridge
Audio Analogue primo cd player with Siltech interconnects

This is my first attempt to set up a decent system, but I recently have run into a problem that I seem unable to fix.

After returning home from a week away with the family, I turned on the amp and after its usual 20 mins warm up hit play on the CD. The sound from the speakers was awful, it was breaking up, distorted and generally inaudible. I checked all the connections and nothing seemed amiss. I changed the input selector to Tuner and tried the turntable, the sound was clear and at least audible but lacked the previous richness of the bass. I removed the turntable interconnect and tried the CD player again, this time it worked but the sound seemed somewhat lifeless and lacking in the pwerful bass that the system had been putting out one week earlier.

One other point that I should mention is that when I bough the Thorens I asked the dealer to custom fit a 2.5m cable from the standard Thorens tonearm. I know that this probably isn't a smart thing to do but this was very much a compromise with my wife to retain the aesthetic look of our living room.

Subsequent actions: I took the amp to the dealer to have all the tubes checked and professionally biased but this did not restore the bass. I checked my speakers with a different amp and they worked perfectly. My question is, could faulty rewiring of the tonearm have caused some damage to the amp when it was connected or is there something else that I haven't thought of? Unfortunately I live in South Korea and do not have the option of sending the amp, which is only three weeks old, back to Audio Research in the US to have it checked.

Any advice or suggestions would be much appreciated.

Did your dealer listen to the amp after they biased it? If it worked well at the dealer but not at your home, it might be something else amiss here.
Thanks for the response:
Yes, after it was biased we listened to it in the dealership and the problem was still evident.
In the VSi-55 you bias the 6550's. Is it possible that one on the other 3 tubes is bad? Have you changed them to different positions?
I checked the other 3 tubes. I don't think this is a tube problem.
The Audio Research folks that answer the phone are really nice and helpful. If they can't answer your question they transfer you to someone that can (they seem to check to make sure that person can take the call too.) I've only called a few times but I have been more impressed with them than any other audio company I've called or emailed.