I've been using my A600 with ACA620 / Indi ECS & Subway/etc for about the last 45 mins. Played a number of WHDLoad Games without issues although I think I was using a beta version of WHDload.
One game crashes (Silkworm) with an 'illegal instruction' error. I updated WHDLoad to 17.1 and now Silkworm is working fine.
@Don try installing WHDLoad 17.1
I'm sure some software will be glitchy with this new hardware, so I expect some stuff just will never work. And that could even be a combination of other issues like Workbench/Kickstart versions.
Anyway, mine seems ok at the moment, let me know how you get on DonAmiga