UEFI install only boots if selected from BIOS

I have recently reinstalled Ubuntu, and now I encounter some issues which seem to be UEFI related. I have tried searching for similar problems, but found no solutions and only one with the same problem, but the topic had no answers..
System
Asus UX32VD, Intel based system with HD4000 + Nvidia graphics.
Problem
The system seems to freeze at "Loading inital ramdisk". It happens both in normal booth (removing quiet splash) and when trying recovery mode. Hence, nomodeset doesn't solve the problem.
How to reproduce
Right after reinstallation the system boots fine all the time. But when I run apt-get upgrade it will fail to boot on the next boot, in both normal and recovery mode. I have resinstalled the system several times, and the same behaviour appears after the upgrade.
Workaround
The curious thing is that if I enter the system setup (UEFI/BIOS-screen), and then select the Ubuntu UEFI boot option, the system boots every time. But if I let the system boot normally, it won't boot. The option I select manually is the same option as the one to boot automatically.
Naturally, I would like to not have to enter the setup every time I use my system. Any idea what could be wrong?