If you only reference the index, and don't specify the desired setting (0/1) then the set message works like a toggle. If you want to use an absolute reference to select the check box, you need to specify:
EnableLimitButton << set(1,1);
Here is the example taken from the Scripting Index, on the Set message usage in the Check Box() object
Help==>Scripting Index==>Check Box==>Set
Names Default To Here( 1 );
New Window( "Example", cb = Check Box( {"One", "Two", "Three"} ) );
cb << Set( 3, 1 );
Jim