TeamSite 7.3.1 issue executing Perl scripts after Windows patching process

So we had a windows patching process last weekend. This patches came by security Team.

Early this monday, incidents begun to raise for workflows not completing and deployments not happening in OpenDeploy (which is one of the tasks of the workflows).

Looking into the logs we found what is causing the workflows to fail:
Workflows are created as WTF and for the content deployment they use Perl scripts (IPL) that use command line executions to generate HTML/XML files, invoke deployment (via iwodstart.exe) and submit the deployed file to staging to generate new versions.
Deeper analysis showed that the execution of the cmd is for example:

my $result    = qx($cmd 2>&1); where cmd is ejecuting X command as for example iwattrib, iwstat, iwodstart, etc.

We found that after the patching process, this execution is not working anymore, it was for years until this weekend.
if we remove the handle redirection for example to:

my $res    = `$cmd`;

then the execution happend properly. however changing all Perl and libraries to validate all scripts using and remove the handle redirection might take a lot of time.
I can also see in the iwutild_cmdout.log the next entries whhen executing the workflows:

The handle could not be opened
during redirection of handle 2.
The handle could not be opened
during redirection of handle 2.

so we have two options:
1.-Request to remove the windows patches installed, however this will lead to more investigation to find out which patch caused the incident and finally try to install solving/preventing the issue. (since those are security patches)

2.-Research what cann be the issue and resolve/fix or ensure it cannot be fixed by any means with latest windows patches.

I've decided for now to investigate the possible causes of the error. I'm going through internet forums posts, looking for errors in handle redirection, perl, windows cmd execution, etc.

At the same time I would like to know if any of you have went into something related or if anyone can share a bit of light on the direction I should investigate. the scpecs of the Install are:

1.-OS: Windows Server2008 R2
2.-TeamSite version: 7.3.1

Notes:
1.-If perl is executed manually on a CMD window the execution happens properly.
2.-user executing the script is returned as teamsitehost$ (where teamsitehost is the acual hostname)