Auto ISO does not work in M mode on the K-r; or at least I could not find it in the manual.
From your initial post, I understand that you want a 'decent' shutter speed and you're 'abusing' M mode for that
I don't have a K-r but can come up with some possible workarounds.
1)
I usually use Av and fixed ISO; when starting I set a reasonable aperture depending on the lens (like f/4 or f/5.6), measure the light by half pressing, and adjust ISO till the shutter speed is what I consider better than acceptable for the lens in question (about 2x focal length). It gives me the flexibility to vary shutter speed depending on the need (either exposure compensation, or an area in the room might be darker than what I measured initially or DOF control).
In your example of the 50/2, I will set it to f/4 and adjust ISO till shutter speed is around 1/90s. This will allow me to go down to approx. 1/20s (which I consider safe with SR).
2)
Use one of the auto modes like Av or Tv and use auto ISO; disadvantage is that the camera might have different ideas of what you have about the combination of shutterspeed and ISO (in Av) or aperture and ISO (in Tv). As you want to prevent shake, Tv might be the way to go; select 1/45s and let the camera decide on the rest.