Resolution of the second monitor is broken after reboot

[Guest]

I faced some rendering artifacts in Chrome(Version 30.0.1599.66). Restarting Chrome did not change anything and I had no time to resolve this issue thoughtfully, so I just rebooted my PC.
After reboot my second monitor resolution has changed to 1024x768, that is not native resolution. I tried to change resolution, but the native resolution disappeared from the settings.
The first monitor works fine. Chrome artifacts also disappeared.

xrandr output:

Screen 0: minimum 320 x 200, current 2944 x 1080, maximum 32767 x 32767
VGA1 connected 1024x768+0+0 (normal left inverted right x axis y axis) 0mm x 0mm
   1024x768       60.0* 
   800x600        60.3     56.2  
   848x480        60.0  
   640x480        59.9  
HDMI1 connected 1920x1080+1024+0 (normal left inverted right x axis y axis) 531mm x 299mm
   1920x1080      60.0*+
   1680x1050      59.9  
   1400x1050      59.9  
   1600x900       60.0  
   1280x1024      75.0     60.0  
   1440x900       59.9  
   1280x800       59.9  
   1152x864       75.0  
   1280x720       60.0  
   1024x768       75.1     60.0  
   832x624        74.6  
   800x600        75.0     60.3     56.2  
   640x480        75.0     60.0  
   720x400        70.1  
DP1 disconnected (normal left inverted right x axis y axis)

For VGA1(second monitor) there are not any resolutions above 1024x768. That is not correct.
Another strange thing that my first monitor is not really connected via HDMI. It's connected via DVI.

I found similar question on askubuntu, but unfortunately it's not answered yet and it doesn't contain any help.

Any help will be greatly appreciated.

Updated: I have just rebooted into LiveCD mode. System detects the same configuration of my displays. Seems like hardware issue. How can I confirm that?