Thank you for the clarification.
Based on the description I can assume that following scenario - There is a MultiSelect control and based on its value the Grid is populated with data. Then the built-in multi checkbox filter is showing only the values from the initial creating of the Grid and it not shown to new Grid value after a new value is selected in the MultiSelect control?
If this is the scenario I tested it and observed the same undesired result on my end as well.
I can confirm that this is an issue with the current version of Kendo UI Grid.
I created an issue in our GitHub repository and forwarded it to our developers for fixing. You can track its progress at:
For now, there is no available workaround, if one is found it will be added to the GitHub issue for reference.
Additionally, I updated your Telerik points for bringing this to our attention.