Might your problem be that system expects a list not a string?

I've had system do odd things in the past due to that!

you could try something like this

my @Jira_command_line= qw/newbug $Jira_bug_category $Jira_bug_number
 trunk $TRUNK $sernum/;
print "Calling '",join(',',@Jira_command_line),"'\n";
$i = system(@Jira_command_line);
[download]

BTW Not Tested at all as I don't run windows here.