The 1.1.4 version just went live which is 3.1 compatible. Just go into Cydia, and you will be prompted to upgrade.

You can also find it in Cydia by going to Keyboards, or on the BigBoss repository

The current 1.1.3 version does not work with firmware 3.1, but we are testing 1.1.4 today (October 4th) which will work with the 3.1 firmware.

Expect the new version in Cydia this week, you will be prompted to upgrade if you launch Cydia. This new version will fix it.