I am having this exact same issue since upgrading to 2015 Q3 SP1. I've created a dojo example using as close our MVC generated grid, and I simplified it as much as possible while still reproducing the problem. Needed to add kendo.aspnetmvc.min.js to includes.
If you look at the bottom of the script , the problem is reproduced:
grid = $(
currOpt = grid.getOptions();
//grid.options = currOpt;
The commented line is a workaround I found - if we explicitly set the options object first by assigning it, THEN call setOptions(), the problem dissapears.
I don't want to go with this workaround in production, however, since I don't understand what it is doing. Please let me know if you can determine what about our grid is keeping setOptions() from working.