Peak meters on the effect rack

To achieve that state, you must have at least one effect in the rack, and if that's creating gain, then yes you will appear to get an overload, at least on the output. But, if you increase the volume in the track, then this increased level is reflected in the effects rack meters, and that will overload both the input and output, unless you reduce the gain.

When it comes to a mixdown, it's relatively safe to leave an overload, as with a Floating Point mix this produces a scaled result that can be rescaled after the event to get the levels back where they should be - looks like magic, but works really well. How this plays with an internal overload though, I'm not entirely sure. It sounds to me as though you need to do a little 'gain staging' here - make sure that with the track volume fader and the master fader set to 0dB that nothing overloads, so no clipping. If it does, then reduce the level of the track so that it doesn't - you can use the volume envelope for this. Then, if nothing is added to the effects rack to increase the gain or level, you shouldn't get clipping any more.

So in bare terms, if you have a track with a volume lift resulting in more that 0dB on the track itself, but with the fader set down so that it doesn't overload the Master, then the track will probably play fine, but the input to the effects rack will clip. And that's what you prevent with gain staging.

I can tell you that there's absolutely nothing inherently wrong with the metering - it's all been thoroughly tested, and it represents accurately what's actually happening in your mix. So whatever's causing this is something you've done, I'm afraid...