The modded SB and linear power supplies do take some time to break-in.
The capacitors used in the power supply take time to form.
One thing that I have found to help speed up the process is to play a full bandwidth signal at very high amplitude
Jim Hagerman's FryKleaner does just that. It is a great product to use for cable and amplifier break-in.
Jim has a .wav file of the FryKleaner "noise" on his website.
http://www.hagtech.com/media/frykleaner.wavIf you take this "noise" and play it on repeat through your SB (with the amps turned off) it should speed up the break-in time.