Great idea - thanks for a fun exercise :) In the spirit of TMTOWTDI, you might consider some of the techniques used below to achieve the same end. It's a little more 'Perlish', and demonstrates a few things - in particular, use of single hashes to replace whole 'lookup' subroutines.

#!/usr/bin/perl

use strict;
use Benchmark;

my @white_keys = (0,2,4,5,7,9,11);
my @modes = qw(Ionian Dorian Phrygian Lydian Mixolydian Aeolian Locria
+n);

my $note = int(rand(12));
my $mode = int(rand(7));
my $pref = qw(# b # b # b b # b # b #)[$note];

my %note2num = qw(C 0 C# 1 Db 1 D 2 D# 3 Eb 3 E 4 F 5 F# 6 Gb 6 G 7 G#
+ 8 Ab 8 A 9 A# 10 Bb 10 B 11);
my %num2note = (($pref eq 'b') 
    ? qw(0 C 1 Db 2 D 3 Eb 4 E 5 F 6 Gb 7 G 8 Ab 9 A 10 Bb 11 B)
    : qw(0 C 1 C# 2 D 3 D# 4 E 5 F 6 F# 7 G 8 G# 9 A 10 A# 11 B));

#rotate white_keys round to right mode
foreach (0..$mode-1) {push @white_keys, shift @white_keys}
my @scale = map {($_+$note-$white_keys[0])%12} @white_keys;

print $num2note{$note}, " ", $modes[$mode], ":+\n";

my $t0 = new Benchmark;
my $cool = <STDIN>;
my $t1 = new Benchmark;
my ($measure) = timestr(timediff($t1, $t0)) =~ /^\s?(\d+ wallclock sec
++s).*/;
my $response = join(" ", map {$note2num{$_}} split(/\s/, $cool));
if ($response eq join (" ", @scale)) {
    print "You're Right! $measure\n";
} 
else {
    print "Sorry $measure\nThe correct scale was: ",join (",",map {$nu
+m2note{$_}} @scale),"\n";
}
exit;
[download]

Of course, the musicologists will notice that the enharmonic equivalents need sorting out - strictly speaking, for instance, Bb Phrygian should be Bb,Cb etc., attempting to maintain the 'always change the letter' directive...I leave this as a further exercise :)

Good luck with the impro - all the best people are jazzers. :)