I had a problem migrating from 1.07 to 1.1.1. (I've read other people are having the same issues) The issue seemed to be related to upgrading some tables.
My workaround was to manually import the migration sql files from the install directory.
I'm on XAMPP on Windows (local install) so I did not run the cli version of upgrade.php.
When importing some files there were errors thrown in relation to the renaming of the tables, lines such as:
RENAME TABLE tu_options TO tu_options_1_0;
RENAME TABLE tu_options_1_1 TO tu_options;
DROP TABLE IF EXISTS tu_options_1_0;
So I renamed those tables manually.
I don't encourage anyone to follow my advice, I'm still not sure my db has been properly migrated or if it lacks fields or even tables (I don't track Fbook or Fsquare for instance, so if anything related to those accounts is missing I won't notice)
Thinkup does not seem to be aware of the problem as it reports the database "is up to date". It is later on when trying to run thinkup when table, and field, not found erros are shown.
So far my install seems ok :o) We'll see... :op
mysqlnd 5.0.8-dev - 20102224 - $Revision: 310735 $
Apache/2.2.21 (Win32) mod_ssl/2.2.21 OpenSSL/1.0.0e PHP/5.3.8 mod_perl/2.0.4 Perl/v5.10.1
Sorry about your trouble. In order to diagnose the problem, we need the exact steps to reproduce the error to begin with. Our automated database upgrade tests work for every version to 1.1.1.