server - What version was installed? x64 or i686? What's the difference exactly?

Okay, so heres my problem.
I recently started migrating several services to individual VMs on my box, using VirtualBox 4.1.

I created a new VirtualBox VM with guest type "Ubuntu (64 Bit)". I've already done this before and it worked like a charm.

I then installed Ubuntu server (12.04) from the exact same dvd image. All the time I thought that it should have installed x64.

I already put a few hours work into the new VM, migrating the webserver and mail system etc.
Today I tried installing a x64 piece of software and it suddenly told me that it needed x64 and I had only i686.

I checked uname -a and this is what it gave me:

Linux hostname 3.2.0-29-generic-pae #46-Ubuntu SMP Fri Jul 27 17:25:43 UTC 2012 i686 i686 i386 GNU/Linux

Any guesses what went wrong? All the time I was thinking I had a x64 system.

Any way to move to a "real" x64?

I have a second VM on this host which is running x64 just fine ..

P.S.: grep --color=always -iw lm /proc/cpuinfo returns lm among the flags.