Not so.

>c:\progs\perl561\bin\perl -le"$x=qr/,/; print for split $x, 'a,b,c'"
a
b
c
[download]

Still not enough information. Don't make us guess, show us some code!

use warnings;
use strict;

my @OuterData = (
    "This  is  some space separated text",
    "On three  different lines",
    "So you can see  what    happens");

my @InnerData = (
    "1, 2, 3, 4",
    "2, 6, 7, 8",
    "3, 10, 11, 12",
    "4, 17, 22, 21",
    "5, B, C, E, F",
    "6, 2, 3, 4, 5");


FileParse('\s+', \@OuterData, sub {
    my @Words = @_;
    my $NWords = scalar @Words;
    print "Line has $NWords words. '@Words'\n";

    FileParse(',\s*', \@InnerData, sub {
        my ($Key, @Values) = @_;
        $Key == $NWords and print join(' ',@Values)," - ";
        });

    print join("-",@Words),"\n";
    });


sub FileParse {
my ($PatternCore, $TextAref, $Code) = @_;
# print "$PatternCore, $TextAref, $Code\n";
my $regexp_p = qr/$PatternCore/;

foreach my $line (@{$TextAref}) {
    # my @Data = split($PatternCore, $line);
    my @Data = split($regexp_p, $line);
    $Code->(@Data);
    }
}

=cut

Perl 5.6.1 built for sun4-solaris

Line has 6 words. 'This is some space separated text'
Argument "1," isn't numeric in numeric eq (==) at pbug.pl line 30.
Argument "2," isn't numeric in numeric eq (==) at pbug.pl line 30.
Argument "3," isn't numeric in numeric eq (==) at pbug.pl line 30.
Argument "4," isn't numeric in numeric eq (==) at pbug.pl line 30.
Argument "5," isn't numeric in numeric eq (==) at pbug.pl line 30.
Argument "6," isn't numeric in numeric eq (==) at pbug.pl line 30.
2, 3, 4, 5 - This-is-some-space-separated-text
Line has 4 words. 'On three different lines'
Argument "1," isn't numeric in numeric eq (==) at pbug.pl line 30.
Argument "2," isn't numeric in numeric eq (==) at pbug.pl line 30.
Argument "3," isn't numeric in numeric eq (==) at pbug.pl line 30.

perl-5.8.8

Line has 6 words. 'This is some space separated text'
2 3 4 5 - This-is-some-space-separated-text
Line has 4 words. 'On three different lines'
17 22 21 - On-three-different-lines
Line has 6 words. 'So you can see what happens'
2 3 4 5 - So-you-can-see-what-happens

And if you really want to have fun:
Try changing my $Regexp_ref;
To: our $Regexp_ref;

Passing the string directly into split seems to work with perl 5.6.1 a
+nd perl 5.8.8
[download]

I can't reproduce your problem with ActivePerl 5.6.1 build 635, but I can reproduce it with ActivePerl 5.6.0 build 623

>c:\progs\perl588\bin\perl 730963.pl
Line has 6 words. 'This is some space separated text'
2 3 4 5 - This-is-some-space-separated-text
Line has 4 words. 'On three different lines'
17 22 21 - On-three-different-lines
Line has 6 words. 'So you can see what happens'
2 3 4 5 - So-you-can-see-what-happens

>c:\progs\perl561\bin\perl 730963.pl
Line has 6 words. 'This is some space separated text'
2 3 4 5 - This-is-some-space-separated-text
Line has 4 words. 'On three different lines'
17 22 21 - On-three-different-lines
Line has 6 words. 'So you can see what happens'
2 3 4 5 - So-you-can-see-what-happens

>c:\progs\perl560\bin\perl 730963.pl
Line has 6 words. 'This is some space separated text'
Argument "1," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "2," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "3," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "4," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "5," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "6," isn't numeric in numeric eq (==) at !.pl line 25.
2, 3, 4, 5 - This-is-some-space-separated-text
Line has 4 words. 'On three different lines'
Argument "1," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "2," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "3," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "4," isn't numeric in numeric eq (==) at !.pl line 25.
17, 22, 21 - Argument "5," isn't numeric in numeric eq (==) at !.pl li
+ne 25.
Argument "6," isn't numeric in numeric eq (==) at !.pl line 25.
On-three-different-lines
Line has 6 words. 'So you can see what happens'
Argument "1," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "2," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "3," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "4," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "5," isn't numeric in numeric eq (==) at !.pl line 25.
Argument "6," isn't numeric in numeric eq (==) at !.pl line 25.
2, 3, 4, 5 - So-you-can-see-what-happens
[download]

The only workaround I've found is to change
my $regexp_p = qr/$PatternCore/;
to
my $regexp_p = $PatternCore;

And if you really want to have fun:
Try changing my $Regexp_ref;
To: our $Regexp_ref;

You mean $regexp_p? No change. my $regexp_p, our $regexp_p and local our $regexp_p all produced the same result.