Yes, please post the complete content of the .bash_profile file (in code-tags...), and if possible, tell us more about how the CentOS 6.3 and the 6.6 machine differ “in terms of the business.” Does one replace the other, are they used for different purposes (as far as Perl is concerned) and so on. Do different users have different profiles, or are these changes applied globally to all users of the machine(s)? Do different users seem to have different Perl-related settings?
Your post certainly suggests that maybe someone purposely installed a different version of Perl on the machine, alongside whatever version is used by the system at large. This might be done, for example, to ensure that a particular application always has known-stable access to a particular version of Perl (and/or package libraries) that it requires ... often, one that is newer than the “system” copy. They would use the bash-profile file to set up environment-variable settings that point to that version. All very, very routine. There might also be profile-variable settings for cpan. (Perl’s contributed-software package manager.) We will know when we see it.
