Hi Jonathan,
To understand if there is a glitch let me first cover how I would recommend doing this and let me know if it does not work that way for you.
1. Open the Layer Settings dialog box and click the layer that you wish to modify so that it is highlighted in the right panel.
2. Now move the left panel and change the number in the last column.
3. Click OK.
See reference image below.
In this way you update the Layer Combination to remember the value of the Intersection Group Number for that particular combination.
Please note that if you wish the Layer Intersection group number to be the same value in all Layer Combinations you will select the layer on the right and then change the value of the number in the left panel in all of the Layer Combinations and then click OK.
If you simply change the number on the right panel and click OK it does not set the value for any particular Layer Combination, it only sets the value for the moment. And as soon as you go to a Saved View with a set Layer Combination, the Intersection Group number will lose the temporary value you had set and change to what is actually stored with the Layer Combination in use by that Saved View.
I hope this helps. Please let me know if it still does not work this way for you.
Best regards,