I just upgraded to the version you released on 10/01, says 45.06.06 (on DNN 6.00.01). I repeated the steps again, same thing. Changes to "Modify layout for: Form Items Layout Text/HTML" do not save. I tried adding a class to the <td> elements. Changes I make in the same Save to CSS Styles do save. No error is reported.
Please try it and if it is saving for you, please let me know. Go in to Modify Form Look and Feel, switch to modify "Form Items Layout Text/HTML" Switch to source/HTML and change