it looks like you are using MySQL or Percona Server 5.0, where LSN is two 32-bit numbers.
xtrabackup_1.3-148.lucid.5_amd64.deb is shipped with two binaries: xtrabackup (used for MySQL 5.1+) and xtrabackup_50 (for 5.0). When you issue innobackupex to create a backup it detects that it has been used against 5.0 and uses xtrabackup_50 to create a backup. That's why xtrabackup fails to read meta-data. Please try to perform an incremental backup with xtrabackup_50.
xtrabackup v. 1.4 and 1.5 provide xtrabackup_51 binary (instead of xtrabackup_50 in v. 1.3). Situation is the same: if you used innobackupex for 5.0, then try incremental backup with xtrabackup_51 - it should work fne.
Since XtraBackup 1.4 xtrabackup_51 binary is used for backups of MySQL 5.0, Percona Server 5.0 and MySQL 5.1 with builtint InnoDB. xtrabackup for 5.1 with InnoDB pluing and 5.5