Interesting fact:
I have netbook (Samsung N308) with dual-boot - Ubuntu (Primary system) and Win7 (secondary system).
On Ubuntu 0.6.0 works fine. On Windows i have the same problem: "Couldn't create atlas bitmap (size 2048X2047).Probably not enough of video memory."

So, i think the root of evil in ...

Thanks, 0.6.0 works fine.

Ubuntu 12.04 Alternate
x0m9k@x0m9k-laptop:~/Games/factorio/bin/i386$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 12.04.2 LTS
Release: 12.04
Codename: precise


x0m9k@x0m9k-laptop:~/Games/factorio/bin/i386$ ./factorio
Cannot load lua script /home/x0m9k ...