Kura

I had a similar issue. Problem was solved by disabling Permissionsbukkit (Via remove from plugins folder) For some reason the version I got was completely broken. It wasn't doing anything. I would suggest trying out each plugin to see what the problem is. Most likely permissions for you too.

Yup. Alt is Invtweak's key for dropping stuff out of your inventory when you click it. Alt+tab seems to get the alt key stuck pressed, and only by repressing does it update. If this is a persistant problem, try rebinding the key.

I found that the best way to fix the world while keeping players happy is simply not deleting player data, only world. Thanks to alchemy bags, you can shift all of your belongings from the old map to the new without too much hassle. I don't think Tekkit 3 will mess with what you had already gathered too much, just mostly add more (Except forestry stuff). Also, don't delete the data folder either. That one has the bag contents, while player folder has all the player data. Side note: My view on restarting from scratch: if you want to do it, hide all your belongings in some chests buried underground in your old base, walk somewhere else, and start over. No need for everyone to start over if you want to.