It's very simple to do search and replace with s/// on simple config files, without using any modules. And you don't need a temporary file either, just load the entire config file into memory, search and replace keys, and write it back to the config file. Perl is great at doing this kind of stuff.

use strict;
use Data::Dumper;

my @config;
{
   local $/ = '[';
   @config = <DATA>;
}

SetConfigKey(\@config, 'bdstest', 'Location', 'Somewhere');
SetConfigKey(\@config, 'bdstest', 'OS', 'WindowsXP');
SetConfigKey(\@config, 'custard', 'MainFunction', 'Perl Perl Perl');
SetConfigKey(\@config, 'custard', 'SCSI', 'YES');

print @config;

sub SetConfigKey
{
    my ($config, $section, $key, $value) = @_;

    foreach (@{$config}) {        # loop through config sections
        next if ! /^$section\]/;  # skip if unwanted
        s/\Q$key\E\s*=.*/$key=$value/;  # replace the value
    }
}


__DATA__
[bdstest]
MainFunction=
SystemType=U5
Env=
Location=
Serial=FW0094810719
Hostid=80c0dc14
OS=Solaris
Version=8
Disk=1x8
Memory=128
CPU=1x360
qfe=
SCSI=
GraphACC=
SupportContract=
#END

[custard]
MainFunction=
SystemType=U5
Env=
Location=
Serial=FW00250126
Hostid=80c0aee2
OS=Solaris
Version=8
Disk=1x8
Memory=256
CPU=1x360
qfe=
SCSI=
GraphACC=
SupportContract=
#END
[download]

And the output is -

[bdstest]
MainFunction=
SystemType=U5
Env=
Location=Somewhere
Serial=FW0094810719
Hostid=80c0dc14
OS=WindowsXP
Version=8
Disk=1x8
Memory=128
CPU=1x360
qfe=
SCSI=
GraphACC=
SupportContract=
#END

[custard]
MainFunction=Perl Perl Perl
SystemType=U5
Env=
Location=
Serial=FW00250126
Hostid=80c0aee2
OS=Solaris
Version=8
Disk=1x8
Memory=256
CPU=1x360
qfe=
SCSI=YES
GraphACC=
SupportContract=
#END
[download]