I think I got it now, thanks to your post Mr. Muskrat. I found that I had to insert an extra parameter to the system call to tell it not to wait for pageant to finish. Otherwise it was hanging because pageant doesn't exit when run without the -c.

Thanks bunches :-)

#!/usr/bin/perl
#

use strict;
use warnings;

system(1,'pageant F:\.keys\acuroot_1_8_12_rsa.ppk F:\.keys\acuroot_1_8
+_13_rsa.ppk');
system('putty -ssh -l root 192.168.100.2 -t -m C:\Users\JWSIMP~1\AppDa
+ta\Local\Temp\BoKFVjf1B9');
system(1,'pageant F:\.keys\operations_rsa.ppk');
system('putty -ssh -l operations 192.168.10.245 -t -m C:\Users\JWSIMP~
+1\AppData\Local\Temp\d60NPopq6A');
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