My method to fix this is to find the setting using the developer tools in Chrome, IE, or Firefox and then apply an appropriate css tag in my site specific css file that I load after bootstrap.
For example, I had to apply this fix to correct a RadComboBox with checkboxes using Bootstrap 3
/* ----- RadComboBox Bootstrap Fix ----- */
.RadComboBox {
border: none;
}
.RadComboBoxDropDown .rcbCheckBox {
margin-top: -3px;
margin-bottom: 0;
margin-right: 5px;
}
Another option is to create custom skin css for your grids and load their css after bootstrap's css file.
If you need a start on creating skins for Telerik controls, see the information here: http://demos.telerik.com/aspnet-ajax/grid/examples/styles/custom-skin/defaultcs.aspx
Pay special attention to Input.MyCustomSkin.css as this can help you set the sizes of your input boxes back to what you want.