I've not had this problem before however I have recently upgraded to Ubuntu 9.04 (from 9.10) and I am using the
newer nVidia drivers (185) so this might be the cause.
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#Output of top#
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
3106 james 20 0 505m 254m 27m S 95.6 8.4 0:48.17 java
2251 james 20 0 353m 89m 30m S 2.0 2.9 3:25.41 firefox
1463 root 20 0 562m 40m 12m S 1.0 1.4 1:27.24 Xorg
Any suggestions would be helpful

Update
The game runs fine, the problem seems to be the mouse input.
Hmm seems to work much better with 'nice -n-20'