In MySQL 5.1, there are two CSV tables in the mysql schema (general_log and slow_log) which are not backuped by innobackupex.pl at all. So when the backup is used to build a slave and 'mysql_upgrade' is run, you get the following error:

<pre>
mysql.time_zone OK
mysql.time_zone_leap_second OK
mysql.time_zone_name OK
mysql.time_zone_transition OK
mysql.time_zone_transition_type OK
mysql.user OK
Running 'mysql_fix_privilege_tables'...
ERROR 13 (HY000) at line 311: Can't get stat of './mysql/general_log.CSV' (Errcode: 2)
ERROR 13 (HY000) at line 316: Can't get stat of './mysql/slow_log.CSV' (Errcode: 2)
FATAL ERROR: Upgrade failed
</pre>

Solution:
Patch innobackup.pl to include CSV tables, specifically line 1449 from
my $wildcard = '*.{frm,MYD,MYI,MRG,TRG,TRN,opt}';


to

my $wildcard = '*.{frm,MYD,MYI,MRG,TRG,TRN,CSV,CSM,opt}';