That should not happen. I don’t see how it can happen - Nyquist plug-ins can’t do that, they can only process tracks that are selected.
By default, if you don’t have a selection in Audacity and you try to apply an effect, Audacity will automatically select all audio tracks (see here: “Select all audio in project, if none selected:”. Perhaps that is what happened.
Assuming that you are using the current version of the plug-in from this topic ReplayGain plug-in (you have not confirmed or denied this), the way that the plug-in is intended to be used is that the effect is applied with the same setting to all tracks that you wish to sound the same loudness. This may be done one track at a time, multiple tracks selected at the same time, or as a “Chain” (batch) process. It is important that the same setting is used on all tracks. The “Normalize” option will then amplify each track to about the same loudness.
After applying the effect, you may use the “Amplify” effect on the tracks, but if you do so the same Amplify amount must be applied to every track.
If you use any compression effect, that should be done before applying the equal loudness plug-in effect and the settings that you use must be the same as you used for other tracks.