What is this mysterious “colouration” that ableton’s EQ Three has with “flat” mode disabled (also the default mode for versions 8 and older) which we hear so much about?
Why does it have a reputation for sounding “bad”?
Analysis provides the answers we seek.
Using the pre/post functionality of my favorite analysis tool, HOFA IQ Analyzer, with stereo pink noise, these images show what is actually happening to our frequency spectrum.
Image 1: No Processing
As you can see, it’s just a flat line straight across, as you’d expect. Good.

As you can see, it’s just a flat line straight across, as you’d expect. Good.

Image 2: EQ Three, Default Mode. Yikes!
FreqLow: 255Hz
FreqHi: 2.55kHz

The problem becomes apparent. We see bumps of 2.7dB right at the crossover. They may look relatively small, but 2.7dB is well beyond the range of perceptibility. Why is this bad?
1: frequencies we probably don’t want to enhance are getting boosted, leading to a tone which is usually not superior than the one started with.
2: phase offsets are occurring (as with any EQ shift), helping to smear and occlude our transients. Not helpful!
FreqLow: 255Hz
FreqHi: 2.55kHz

The problem becomes apparent. We see bumps of 2.7dB right at the crossover. They may look relatively small, but 2.7dB is well beyond the range of perceptibility. Why is this bad?
1: frequencies we probably don’t want to enhance are getting boosted, leading to a tone which is usually not superior than the one started with.
2: phase offsets are occurring (as with any EQ shift), helping to smear and occlude our transients. Not helpful!
Generally, the frequency crossovers are going to be set so that the lows, mids, and highs are working on frequencies you want to work on. Therefore, these bumps at the crossover points are going to be exactly where we don’t want them. The exception would be when doing a steep shelf cut of the lows or highs; in these cases, having the crossover bump might be quite useful for enhancing the cutoff point (for example to reduce sub mud while retaining the punch of the bass fundamental).In our example with cutoffs set to 255 and 2.55k, let’s say we want to use an instance of EQ3 to boost the brightness above 2.55kHz. We do so, but also find ourselves with boosts at 255 and 2.55k. This is not what we want.Image 3: EQ Three, Flat Mode. Wait a sec…

OK, this looks better. But wait! Look closely… see a little dip at 255Hz. It becomes apparent that even the “flat” mode of EQ Three (deliberately in quotes) is not perfectly neutral. Dang!
Here’s that section zoomed in closer…

I’m sure it sounds better than the non-flat mode, since it’s just a light smooth dip of less than 1dB in the lower crossover and softening low-mid mud a touch can generally help raw recordings, but it’s still. Not. Perfectly. Flat. What the..!

OK, this looks better. But wait! Look closely… see a little dip at 255Hz. It becomes apparent that even the “flat” mode of EQ Three (deliberately in quotes) is not perfectly neutral. Dang!
Here’s that section zoomed in closer…

I’m sure it sounds better than the non-flat mode, since it’s just a light smooth dip of less than 1dB in the lower crossover and softening low-mid mud a touch can generally help raw recordings, but it’s still. Not. Perfectly. Flat. What the..!
In Summary
Don’t use EQ Three for surgical treatments. At all. Only use it for characterful coloration, and use it very carefully. Keep that slight low-mid crossover dip in mind. I would recommend only switching flat mode off (or using EQ Three at all in older versions than Live 9) if you plan to use both a low-shelf cut and a high-shelf cut (with a mid boost or not), while retaining punch at the corners. For any other purpose, i would not recommend it.
I have a feeling that this might be one of the reasons why Ableton acquired at some point a reputation as being inferior audio-quality-wise to some other DAWs. If you had a session populated with loads of instances of EQ3 (particularly in live 8 or older), there would be tons of ugly unnecessary EQ bumps all over the place which you might not notice immediately but which would result in all sorts of tone and phase wonkiness in the mix.
Don’t use EQ Three for surgical treatments. At all. Only use it for characterful coloration, and use it very carefully. Keep that slight low-mid crossover dip in mind. I would recommend only switching flat mode off (or using EQ Three at all in older versions than Live 9) if you plan to use both a low-shelf cut and a high-shelf cut (with a mid boost or not), while retaining punch at the corners. For any other purpose, i would not recommend it.
I have a feeling that this might be one of the reasons why Ableton acquired at some point a reputation as being inferior audio-quality-wise to some other DAWs. If you had a session populated with loads of instances of EQ3 (particularly in live 8 or older), there would be tons of ugly unnecessary EQ bumps all over the place which you might not notice immediately but which would result in all sorts of tone and phase wonkiness in the mix.