The installation dir just looks fine to me. I have more versioned directories from 5.8.3 to 5.8.8. But yours look like come from two different version of Perl. On my machine,

$ perl -v
This is perl, v5.8.8 built for i386-linux-thread-multi
[download]

When I peek at the source of cpan, command line the shebang points to /usr/bin/perl, and,

$ head `which cpan`
#!/usr/bin/perl

eval 'exec /usr/bin/perl  -S $0 ${1+"$@"}'
    if 0; # not running under some shell

$ /usr/bin/perl -v
This is perl, v5.8.8 built for i386-linux-thread-multi
[download]

Both commands gave me the same version of Perl, so the @INC should stay same. Either cpan or manual installation will go to the same installation dir. Could you reproduce those commands on your machine?

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