Hi,
The easiest solution for now is to add the missing columns to database using phpMyAdmin and running the following SQL (replace {prefix} with your Joomla DB prefix):
ALTER TABLE {prefix}_sefurls ADD COLUMN `metacustom` TEXT, ADD COLUMN `trashed` TINYINT(1) NOT NULL DEFAULT '0';
Then run import (make sure you use the Import button in JoomSEF's Manage SEF URLs page toolbar). After the URLs are imported correctly, run the following SQL to remove the columns again, so you won't have problems updating JoomSEF in future (replace {prefix} with your Joomla DB prefix):
ALTER TABLE {prefix}_sefurls DROP COLUMN `metacustom`, DROP COLUMN `trashed`;
We'll fix this incompatibility in next version.