The CR emulates the serial connection a little different, maybe that's why your preferred programs dont work, I haven't used those programs so I don't have any advice there.
Putty works. Not sure what else to suggest, maybe write your own format in the CR firmware and work with that.
A nice GUI that is customizable would be great, to control logging output etc, then the CR would not need to keep time or timestamps, it doesn't even make sense, or it would require an RTC and also it would greatly increase the serial output bytes.
I talked to the creator of CurrentViewer about how we can increase the SPS and improve that GUI. An ideal SPS target would be 1kSPS perhaps achievable with some new techniques of sampling and streaming the data. Unfortunately I think he did not wrote this for Windows. And this is just a side project whenever he has time (and me as well!).