Are you using Windows? If so you can use a registry tweak to change the window size.

1. Close Spiral Knights (if it's running).
2. Click on the 'Start' menu and then click on 'Run'.
3. Type in "regedit" and hit 'OK': this will bring up the Registry Editor. Warning: Please do not change anything else in the registry since it could cause severe problems.
4. Browse through the registry tree and expand to 'HKEY_CURRENT_USER\Software\JavaSoft\Prefs\projectx'
5. Look for the value "display_mode" and double click it.
6. The first two numbers represent window width and height. Set these values to what is desired. NOTE: Only values seen in the in-game drop box will work. Others will be ignored.
7. Close the Registry Editor and start Spiral Knights.

(this was adapted from section 5 of the Technical Help Sticky

For what it's worth, you should also try to seek out a driver update for your graphics card.