As we have found out, the original custom script was written by Softaculous. The encoded files were encoded by your team. We paid you for this special custom installer, but you never provided UN-encoded files as part of our purchase.
We see a lot of differences now since this update, and thus it is completely broken even when moving the proper files from Wordpress, as something within your custom files is breaking now.
We have a ticket open with you (ticket #726079), as we are still having issues and the custom script is completely broken. This has completely taken down our business.