I'd also not used Chomp for a few years, but I just reinstalled it to test and for me it behaves like every other SMS app: threads are ordered by the most recent message in each (which is also how it always used to work).
On a quick scan I've not spotted any obvious setting to change this. So just a guess, but is there something funny about the messages themselves? Does the "new" message have a time in the past, or do you have other threads whose most recent message has a time in the future? It's only speculation, but if the message time got messed-up somehow then this could result in the sort of thing you describe. Depending on the pattern I can think of different scenarios for what would have to be corrupted, though if many threads appear before the new message then if this is the cause it would imply that something happened on your device, e.g. the times of your replies are wrong or at some point the times of everything got messed-up and so newer messages appear to be older than existing ones.
Just trying to come up with an explanation here, I don't know whether this is the case. But maybe check the times/dates of the "new" messages and compare to some of the older ones that are appearing above them? And also check your system clock, in case that's got the wrong time/date/year and that's causing new message to appear old?
