Please search AutoConfig log file for ouicli.pl and you should find more details about the error.
R12 with DB 11.2.x: RC-50013: 'Instantiate driver did not complete successfully.' 'Perl lib version (v5.8.8) doesn't match executable version (v5.10.0)' (Doc ID 1333997.1)
Rapid Clone on dbTier fails: "RC-50013: FATAL: INSTANTIATE DRIVER DID NOT COMPLETE SUCCESSFULLY." (Doc ID 1063772.1)
Troubleshooting RapidClone issues with Oracle Applications R12 (Doc ID 603104.1)
Just before running the post clone script on the DB tier, try running the Source DB enviornment file which is been copied to the target instance.
Probable reason: Perl command uses older version which is picked by OS, and when you run the DB enviornment file it uses the newer release of the Perl version.