@fentimanj hi! Let's continue the discussion here as I just posted on Amiberry's github. First of all I need to ensure you've read the "main" thread about Amiga and Amiberry (here). Then I'd need more inputs about your setup. For instance, which Retropie version you're using, have you updated the OS packages and/or Amiberry, etc? A full description about your setup always help as said in that post ;-)
If you got Amiberry logo and WHDload Autobooter screens this is not good. Especially for a game like Lotus 2 which has been heavily tested. Therefore I suspect you either do not have the very latest version of the WHD package of that game (should be Lotus2_v1.11_0497.lha as of typing) or you renamed the file. If you did the latter please don't and leave the name as-is.
Without further details from your setup I can't help much. Just ensure to get the latest Amiberry binary from Retropie Setup (or compile from source), check the names of your packages/.lha files and also double-check the Kickstart ROMs you got. They must match those listed here.
@adambegood I'm also experiencing intermittent results from Auto height. I don't have Rick Dangerous 2 but Shadow of the Beast works fine for me.
Now that I've got the latest Amiberry after updating from Source, Shadow Of The Beast works fine for me also. I have some games with anomalies on auto-height still, but overall I am very happy with the way things are working.
On a slightly different note, I have got some games with graphical glitching (Deluxe Galaga and Plan 9 from Outer Space are the ones I recall). Do you know if there are any settings that might sort those out, or is it just something that has to be accepted?