That's exactly what I'm saying. I currently have 3 other drive pedals after the Fliptop Boost and it's the same on all of them. It's definitely the Fliptop Boost clipping, as it has a very distinctive non-pleasant 'electrical shorting' type of clipping. It does not clip my RFE, Diamond Bass Comp, or MonoComp which are all after it also.
All that being said, I've only tested this through headphones and my USB audio interface. Maybe it's something with that, but I have they are not clipping as I can replicate it with very little volume and negative overall gain.
More experimentation is needed here. I really think it's the input of the Fliptop Boost that's clipping, but it's so odd that it only does it when driving another pedal. If I lower the volume on the bass, it clears up.