With Geany 1.28 Release for all three file types as attached above the status bar shows the mode correctly (mode:CR / mode:CRLF / mode:LF).
Current Git 2a2ae72 on Linux gets all three right, so its something strange about Windows or nightly builds.
The code for determining the line ending is [here](https://github.com/geany/geany/blob/master/src/utils.c#L102) and as you can see its not related to Windows or Linux. I notice it has a bug where it will undercount CRs for successive blank lines in CR only files, but thats not this. I am not aware of any change here lately, but your nightly is a couple of months old, you might try the latest.