What brand tubes did your phono stage come with?
My Io phono stage (purchased in 2006) came with a set of Sovteks and for the V1/V2 they were 12AX7LPS. The first stage in these phono amps are the most critical for low noise tubes. The tubes may have tested low noise, but they may have drifted from specification after a period of time, resulting in noise. Sometimes, this can occur in a short period, which is rare. I had direct experience with this scenario and replaced with a different set of tubes and voila, no more noise.
Would recommend replacing the V1/V2 stages if so configured with the exact tubes in low noise/low microphonic from either Aesthetix or a reputable dealer.