One key point not mentioned: A radio altimeter measures geometric height and an altimeter measures pressure altitude.
Now when you are at ISA those should go together. But as i understand it and very simply put: When the temperature is higher than standard then the air is less dense so you need to "stack" more of it to get to the according pressure. And when the air is cold you need to stack a lot less. Now this also applies to differences in altitudes.
If the air is warmer than ISA you will be further than 1000 ft apart flying at pressure altitudes that are 1000 ft apart.
Now if the air is colder than ISA which probably was the case with your example than you will be closer together.