upgrade problem using wpau

Several weeks ago I tried to upgrade my site using the wpau plug in, something I have successfully used for years. However, the process crashed my site. Subsequently I tried multiple manual upgrades over the original install including the original data base, all of which failed.

After checking my databases and the config files I found that the config files while correct had been misdirected to the wrong data bases.

Finally, after a completely fresh install of ver 4.0 using a new database the site loaded.

My question is: have there problems upgrading after ver.3.6 using wpau?
Also, I’ve seen references to a new automatic upgrade in later versions how does that work and have there been problems with that?