We just could not crack it so deleted everything and did a fresh install of V 1.5.4.
We do however have quite a few ZenCarts V1.3.9 we need to upgrade to V1.5.4 and not looking forward to this.
Have discovered an added problem in that V1.5.4 needs PHP V.5.4 but versions 1.3.9 will NOT work with this so upgrading the server to PHP5.4 will knock out all older versions of ZenCart.
The work around is to alter the .htaccess file and add in a php.ini file. All an added complication.
We host with Bluehost but they won't discuss any ZenCart problems with you unless you installed ZenCart using their MOJO software and will not support any installations done manually with FTP upload (we use CoreFTP).
As we take payments by PayPal Express and Nochex we never receive any of our customers payment details ourselves so don't need a Certificate but Bluehost do everything they can to force us to buy one but having over 30 ZenCarts this would add to our costs considerably each year.
They tried putting one of our ZenCarts onto a VPS where we were entitled to a free certificate but we found while we could access the storefront the link to the admin area no longer worked so had to revert back to a shared system.
soundcatcher:
I just wanted to post a reply in here to hopefully aid with working out what is causing this issue...
I have been battling with this exact same issue for several weeks to no avail.
This morning I tried changing the admin password and re-trying the database upgrade and it worked! :-)
I didn't at any point login to admin or access storefront during the upgrade process from v1.5.3 to v1.5.4
Oh I have been using PHP version 5.5 all the way through.
This is all a bit of a mystery to me as to why it didn't work originally, but this fix worked for me!