I've never used Softaculous, but I have seem other reports of people have trouble after upgrading or installing with it.
Updating copies a bunch of new files into position, so it could result in a missing or corrupted file or changed permissions/ownership. There's also a possibility that some files that should have been overwritten weren't -- leaving you trying to run a mixture of old and new code.
Though less likely, updating could also reconfigure paths or media sources, depending on what version you upgraded from.
If it's mod_security, it would have to be a coincidence.
I think what I would do next is to download the exact same version of MODX to your local machine and install it. Then copy the ext-all.js file to the remote. If you still get the error, you know it's not a problem with that file.
