There is a buzzzing noise that can happen if your DSP load gets too close to 100%. Plogue can't keep up with everytihing you're asking it to do in realtime.
Assuming that is the problem, you should do the measure levels and apply gains passes in offline mode (It's on the Plogue Edit menu). That turns off your audio output and Plogue can take as long as it needs to process because you're no longer in real time (with the sound off). Also in offline mode you don't need to worry about running other things on your computer while you're converting with SPEC. In online mode you could cause Plogue to glitch if you start up a heavy CPU or Disk I/O process.
Other ways to reduce DSP (without going into offline mode) are to reduce your FFT size and/or overlap settings. That can result in a lower quality conversion, however, and that's why using offline mode is a standard practice.
If the DSP buzz is not what you're hearing, you should check for clipping at the different parts of the layout. Everything Plogue native can go up to +10dB without distortion but that may not be true of VSTs included (and definitely not true of recording in 24 bit fixed format) . Right clicking on a group or bidule (the boxes) and selecting monitor will let you see the inputs and outputs of each group or bidule. Set the pregain in SPEC so that the Center (usually the loudest channel) never goes above 0dB. If you do that every thing else in the chain should be OK but it won't hurt to check.
A burst of white noise would normally only come from a trial version of a VST you added to the layout. Some of them add bursts of white noise or go silent to force you to spam the full version.
Oh, there is a source of white noise in SPEC. In the normalize group. That should never get into the audio chain unless you change the wiring around. It's purpose is to provide a constant 0dB signal to ZAG (in place of the original stereo signal) when you are doing a compilation album or want all tracks to be at the same volume (vs. each track have the same relative volume as the original album).
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