Magento – Magento & Paypal IPN problems & failiure

We upgraded to paypal pro and then we start receiving IPN problems.
We are receiving IPN warning emails from paypal and we continue to get problems where: paypal receives the order information but nothing is confirmed back to our Magento database. The IPN history report from my paypal shows IPN retrying and failiure.
On all the retry/failiure status we have no order recorded in Magento but we do have the paypal payment.
It seems that Magento says processing payment and then returns to the shopping cart and does not show the Magento completed transaction page. Therefore the information goes out but the IPN does deliver back from paypal in our Magento.

Here is what our server side have commented;
We can see the following messages when the IPN requests are being served:

[22/Jan/2014:09:39:10 -0600] "POST /paypal/ipn/ HTTP/1.0" 503 – "-"
"PayPal IPN ( [link removed] )" [22/Jan/2014:09:44:31 -0600] "POST
/paypal/ipn/ HTTP/1.0" 503 – "-" "PayPal IPN ( [link removed] )"
[22/Jan/2014:09:55:12 -0600] "POST /paypal/ipn/ HTTP/1.0" 503 – "-"
"PayPal IPN ( [link removed] )" [22/Jan/2014:10:16:33 -0600] "POST
/paypal/ipn/ HTTP/1.0" 503 – "-" "PayPal IPN ( [link removed] )"
[22/Jan/2014:09:31:16 -0600] "POST /paypal/ipn/ HTTP/1.0" 503 – "-"
"PayPal IPN ( [link removed] )"

As per the logs of the suexec log on our servers (the service that executes your PHP scripts):

Code:

[2014-01-22 10:16:28]: info: [usr/grp]: cucumber/cucumber cmd: /home/cucumber/public_html/index.php php: /usr/local/php53/bin/php
[2014-01-22 10:16:28]: info: [usr/grp]: cucumber/cucumber cmd: /home/cucumber/public_html/index.php php: /usr/local/php53/bin/php
[2014-01-22 10:16:30]: info: [usr/grp]: cucumber/cucumber cmd: /home/cucumber/public_html/index.php php: /usr/local/php53/bin/php
[2014-01-22 10:16:33]: info: [usr/grp]: cucumber/cucumber cmd: /home/cucumber/public_html/index.php php: /usr/local/php53/bin/php

I can also see that in some cases the requests are processed properly, which is quite strange:

Code:

[22/Jan/2014:08:12:05 -0600] "POST /paypal/ipn/ HTTP/1.0" 200 - "-" "PayPal IPN ( [link removed] )"

The requests have been served properly by our server, since it executes the index.php file and it seems that the 503 error message is being returned by the Magento application itself, but not by our server.

If the message was being returned by our server, the index.php script would not be executed at all.

I am stuck with the next action in resolving this, any comments would be appreciated.