I use an Optimus notebook and can't use official Nvidia drivers with Bumblebee. Also drivers newer than nvidia-331.38 in software center had issued with Boinc saying Nvidia library present but no GPU's. Finally solved my issue and running Boinc with nvidia-343.21 driver from Xorg-edgers... Problem was update-alternatives thing. I had set it to use mesa drivers because of sound issues in Skype. Now when I switch it to Nvidia-343 drivers Bumblebee can run Boinc without any issue.

The command used to set it is:
sudo update-alternatives --config x86_64-linux-gnu_gl_conf
There I chose nvidia-343 and its OK.
Now, the current issue is everytime I reboot, the setting is returned to mesa and I had to set it nvidia manually again. How can I fix it, or what's changing it?

Command display:
There are 3 choices for the alternative x86_64-linux-gnu_gl_conf (providing /etc/ld.so.conf.d/x86_64-linux-gnu_GL.conf).

Seçim Yol Öncelik Durum
------------------------------------------------------------
* 0 /usr/lib/nvidia-343/ld.so.conf 8604 otomatik kip
1 /usr/lib/nvidia-343-prime/ld.so.conf 8603 manuel kip
2 /usr/lib/nvidia-343/ld.so.conf 8604 manuel kip
3 /usr/lib/x86_64-linux-gnu/mesa/ld.so.conf 500 manuel kip

Also I forgot to mention in the previous message that I had to install NVIDIA MODPROBE package so that Boinc detects Nvidia GPU and Cuda. Else it says drivers present but no GPU.