Sounds like there are a few different problems here. For the Scoot stage drifting up, you need to fix a length for the stage without a Scoot loop. I would set the stage min and max to the fixed value you want. Also on the network data, there is an option to mark a stage as fixed length, this should be selected for the stage in question. Finally check none of the links have ticked the fixed length stage as being associated with the link, note the fixed length stage doesn’t require a link to be defined (we run an Imtech server but I assume options would be similar for both types).
As to the unpredictable intergreens, sounds like there is something funny in the controller config. We had a couple of sites that gave similar errors, one reverted to all-red but there was no all-red stage G-bit, so this gave long intergreeen errors, or no road green confirm errors. You mentioned demand dependent stages, but are all your phases type 0’s? Sometimes setting demand dependent phase types can give issues if all phases need to be at ROW before the G-bit replies. If you can post the controller config, I could have a look and advise further.