Assuming your examples are definitive, this GRT should work for you:

#! perl -slw
use strict;
my %months = (
    FY => 0,
    Jan => 1, Feb => 2, Mar => 3, Apr => 4, May => 5, Jun => 6,
    Jul => 7, Aug => 8, Sep => 9, Oct => 10, Nov => 11, Dec => 12,
);

print for map{
    unpack 'x[nn]A*', $_
} sort map {
    my( $alpha, $num ) = m[^(\S+?)\s*(\d+)$];
    $num += 2000 if $num <= 49;
    $num += 1900 if $num <= 99;
    pack 'nnA*', $num, $months{ $alpha }, $_;
} <DATA>;


__DATA__
Apr 2006
FY05
FY98
FY04
Dec 2007
Jan 1997
Jan 1998
Dec 1998
[download]

Output

C:\test>junk
Jan 1997
FY98
Jan 1998
Dec 1998
FY04
FY05
Apr 2006
Dec 2007
[download]