Comment 5 for bug 839306

That's expected behavior. On the first pass XtraBackup wants to replay the backup log, so it modifies log files configuration to match xtrabackup_logfile parameters. The second pass is used to pre-create InnoDB log files, so it uses real values read from configuration file.

So I'm not sure what specific problem we are chasing here. You mentioned that xtrabackup failed to get the correct innodb_data_file_path value from my.cnf. So does the crash occur with xtrabackup is doing recovery with a wrong value?

Can you paste the output of "xtrabackup_55 --print-param"? Does specifying --innodb-data-file-path explictly on the xtrabackup command line solve the problem?