That makes sense, the standalone software was giving varying latencies when it was processing, which live's compensation could not acount for since it was external.
Out of curiosity, are you able to use the arp beat sync quantize function? i never got it to work when clocking externally from midi, i found just starting/stopping the sequence manually in time much more consistent.
You can use one of the cv inputs, or the ext input to trigger the sequener. I've never tried this tbh. But if you set the sequencer to trigger mode and select the play source to be ext in or cv, the sequencer should advance one step each time the Pro 3 receives a trigger. Not sure how it will then deal with notes that are longer than the main step length, or ratchets, though.
I think if you don't have any cv/eurorack gear that can convert a clock or a dc coupled output with cv software, You could use the oldschool approach of a very short audio click going into the ext input. This way it will follow the latency compensation tightly , and it actually works lexactly like those super expensive clocking devices like from ERM.
I remember doing this on my original SH101 and being very surprised at the rythmic tightness it provides.
One Ableton related thing: i found that Live has some latency on midi note input playback, even on internal plugins as soon as latency compensation is enabled. Selecting 'low latency when monitoring does improve things, but turning off latency compensation is still noticeably snappier.
Personally, i found setting a low buffer size, and disabling latency compensation gives me the easiest way to have a creative workflow with a hybrid setup. If not, i need to constantly adjust both audio and midi clock delays when i switch from using the external sequencer vs playing notes from the DAW. Just disabling latency comp allows me to have a setting that is tight enough for realtime composition. I only enable the comensation once i'm fully recorded in the DAW and the high latency mixing/masteering plugins get used.