Can you isolate the problem at all?
- Do you still have a problem with the EQ on vs. off?
- Is the noise heard on the preamp out?
- Is the noise heard on the DI... pre vs post settings?
- Is the noise present if you use another preamp into the power amp in?
- Noise present on all frequency knob settings?
- Is the peak LED lighting up?
- How is the sound from the tuner output? This is buffered directly from the input jack it should be nice and clean.
If it seems like a tube, try swapping one at a time.
Use the block diagram on page 13 to help you isolate the problem: http://www.ampeg.com/pdf/SVT-3PRO_OM.pdf
I had a similar problem on a Trace Elliot amp. It turned out to be a cracked solder joint on the input jack and a dirty tube socket. The cabinet vibrating the amp caused the amp to fail intermittently with a slight loss of volume and a fuzzy tone.
Best of Luck.