For all that is holy...
It has been a while (as in years now I think...) since the distro has been updated and a current iteration done.
any number of things could be the issue consequently...
Even still...my best suggestions are 3 things...
1- find if anyone here has kept a version updated...and grab a copy...
2- muck about with it yourself..
3- wait for me to do a current version

Now since it has been a while ...
Just a thought....
If you are using it on usb only...
you did read that you need to enable "persistence"

You have turned "persistence" on ...correct?
that alone is the biggest culprit...(forgetting that setting..)
for working "on" a usb drive and retaining your work....
you may wish to "turn the switch on"
that is also one of the reasons why I suggest multiple copies...
ALWAYS keeping at least one copy that is pristine ...
un-frakked-up...

and various other copies at different states of devel...as precautionary... in case you muck up your own work...
Of course there are back ups and all such goodies on the distro ...
But one can never have enough back up protocol.

What to do if you wish to install it to hdd???
the instructions are plain...
and haven't changed as far as I know.

Just Install it.

simple...

Personally I never had the problem you are expressing ....concerning using a usb drive.
and frankly...
I have used it more often ON a hdd which it was installed to.....
more often than not..


I am betting the problem is...you didn't enable persistence....
why else would it appear to automatically revert the usb to the exact original settings? with the loss of whatever changes you made...?
That is a "persistence" issue with on the usb.
Or rather lack of persistence...
It may also be that the usb is the prob...
or how it interfaces with the computer...
or the distro needs updating..
or countless other possible permutations...

it seems to me though....
to be an issue which points directly to persistence setting not enabled or not functioning properly.
dead flat simple.