adb backup on Marshmallow - is it different?
Same problem here - this is how I fixed it on my side.
Preparations:
- Samsung Galaxy S5 on Android 6.0.1 (not rooted)
- adb v. 1.0.32 running under Windows 10 command line
- password set on the S5  

I succeeded when using quotes for all switches:
adb backup "-apk -noshared -all -nosystem"
-> will prompt for the password and produce a backup.ab  

To backup single apk using a custom file name:
adb backup -f all_apk_obb.ab "-apk -obb com.estrongs.android.pop"

Seems that the switch handling of adb is a bit weird in the latest releases.
I did that before and my old scripts are not working anymore.