WordPress upgrade from 2.7 to 3.3 Permalink problem

Never try to upgrade that many versions in a single step! You will need to carry out a series of smaller, manual, upgrades:
2.7 -> 2.8 -> 2.9 -> 3.0 -> 3.2 -> 3.3.1 ->3.3

I would deactivate all plugins and switch to default theme
when you get to current version, switch themes to what you are using and see if it breaks – if so, it will need to be updated
– start activating plugins one by one to make sure they work – I’m sure all of them will prompt for an upgrade – you should do that 1st