We tested it on some more installations and we can reproduce it even on modx 2.x with cb 1.12. It only occurs if the template gets inserted into a non-empty ressource, if there is no other layout present, it works just fine.
I don’t know what to say - I can’t reproduce this. I’ve tried on 2 more sites, one on 3.1 and one on 2.8 and it’s inserting in the right order in all cases with existing content or empty pages. Using Firefox.
There must be another factor interfering. Perhaps other plugins, browser extensions, custom input types?
Want to send me a login (support@modmore.com) for one of the sites you’re seeing this behavior on so I can check that out?