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anything in the error log?
which browser do you use? you should be able to open the console of the browser before you run the upgrade and see if any errors are thrown in the console for any of the ajax responses...
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Can you clear the log and run the upgrade again following the same steps as before and see if any new items get added. But just focus on the errors - leave out the CSS which takes up so many lines!
So what is this tool? Is this something in IE?
And - after you have done the above could you perhaps also look at the server php log which also might yield a clue...
YELLOW
SWORDFISH
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That is the only js errors that come up on the firefox console
[16:33:30.092] Use of getAttributeNode() is deprecated. Use getAttribute() instead. @ http://www.autismnetworkscotland.org.uk/wp-includes/js/jquery/jquery.js?ver=1.7.2:2
[16:33:30.092] Use of attributes' specified attribute is deprecated. It always returns true. @ http://www.autismnetworkscotland.org.uk/wp-includes/js/jquery/jquery.js?ver=1.7.2:2
will try and get the php error log
While I do not believe this is really the problem we may as well at least explore it so - is your test environment also running WP 3.4.2?
It IS worth noting however that we often need to make a lot of code changes to support new versions of WordPress not least because WP supplies core JavaScript libraries which also change quite rapidly. Your current environment is running a 1.7.x version of jQuery whereas WP 3.6 due to be released some time this week is now using 1.10.2. The same rule will apply to other plugins as well. It is probably, as a rule of thumb, unwise to update plugins that are newer than the core WP the site uses.
It just looks like here we need to determine the difference between your live environment and your test server and why the live server appears to not allow you to make SQL schema changes - assuming you do actually have mySQL permission to make schema changes.
So - anything in the php error log?
YELLOW
SWORDFISH
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