The entries you are missing in your output seem to be the numbers denoted by 'SW:'.
Neither of your regexes attempt to match for this at all. The 'SW;'
numbers also seem to have a unique trait that spaces are allowed as part
of the data. 'SW: 1.00.00 S'

The following is a modification of your loop that gives the output you specified.

while (<DATA>) 
{
    push @array, $1 if ( /Version:?\s*([^\s,]+)/i );
    push @array, $1 if ( /SW:?\s*([^\n\r]+)/i );
}
[download]

Outputs:

:!./test.pl
$VAR1 = '12.2(15)T8,';
$VAR2 = '2.2.0.1';
$VAR3 = '9.0.0.2';
$VAR4 = '6.3(7)';
$VAR5 = '5.0.0.3';
$VAR6 = '2.1.2.1';
$VAR7 = 'E5.8.0.3';
$VAR8 = '1.00.00 S';
$VAR9 = '12.0(14)';
[download]

Hope that helps.

Wonko