Although it may be an option, when InstantCake is used, AFIK it always sets a variable to disable automatic updates.
As long as you installed PTVNet at the same time, you can buy the Slicer from dvr upgrade and use it to upgrade to a later version of the software.
There is an article on the dvr playground forum that describes how to use the Slicer to upgrade a box to upgrade to 6.3b. You just need to use the name for the 6.3e slices instead of the 6.3b ones and the upgrade works fine.
Don't try to apply the patches mentioned in the article for HMO/HME and MRV. The patch addresses for HMO/HME are not the same under 6.3e and the code that allowed patches to enable MRV under earlier versions appears to have been removed completely from 6.3e.
I never tried any of the patches myself, since I make too many typing errors for it to be safe, but I have used the Slicer to upgrade from 3.1.5f to 6.3c, 6.3d and 6.3e with no problems.