Here's the filters, unfortunately I do not have time to measure anything. I read some reports from other users which states that clipping and artifacts can occur with EQ if the master gain is not matched (in negative) of the highest filter gain. I tried to lower the master gain on the generated EQs and the clipping was gone.
Coincidently, I just discovered a related bug in my script, I was rounding the preamp to the nearest integer, but I should have been taking the floor (i.e. rounding down, which is what an older version of the script did). However, this doesn't affect the filters you gave me (as rounding and flooring produce the same result).
As such, I was unable to reproduce any issue using my FiiO Melody (looped back into itself, sample rate 44.1kHz)
As you can see, no clipping, and identical to Equalizer APO.
So my guess is you have the same problem as my Tiny A has: the master gain is capped at a value less than the maximum (i.e. +12dB).
So I can update my script to fix this automatically, if you could please find the
minimum value for the master gain that produces output at the same volume as the EQ disabled. For most devices this is +12dB, but for my Tiny it is +5dB.
(Just reset the EQ to get a flat EQ, and then adjust the slider, switching the EQ on and off until your ears can't tell the difference)
To be sure they are at the same volume, you can measure the result with REW, or just any sound recording program really.
If you do find that +12dB is the value that gives the same volume as the EQ off, then I have no idea what the issue is unless you do take the time to measure the frequency response like I did above.