Duplicate cron runs

I have a website hosted with Omega8 (Pressflow 6.30 (issue persists on 6.31 as well), nginx, PHP 5.3.28, MariaDB 5.5.37), they have a unique setup built specifically for Drupal. The website has worked fine for 3 months, but at the beginning of April our customers started receiving duplicate emails. I replaced the Messaging and Notifications modules with Subscriptions, but the issue remained. Then it turned out that it was due to duplicate cron requests - Omega8 doesn't allow remote cron requests, they are generated locally instead - and for some reason they were generated one right after the another.

Here's the comment of the tech support: "My guess is that the initial slow response from the site's cron request allowed system level tasks queue to invoke another request before Drupal was able to recycle its cron semaphore. That said, no matter how fast the cron requests/sequences are, Drupal shouldn't allow that. ... it looks like either core bug or something in your codebase which triggers or causes semaphore to be less reliable for some reason. We couldn't determine the exact reason yet."

Here are some of cron duplicate request logs:

"134.19.164.53" rusmininfo.com [30/Apr/2014:10:59:01 +0100] "GET /cron.php HTTP/1.1" 200 5 82 357 "-" "iCabPro" 0.028 "-"
"134.19.164.53" rusmininfo.com [30/Apr/2014:10:59:09 +0100] "GET /cron.php HTTP/1.1" 200 5 82 357 "-" "iCabPro" 43.676 "-"

"134.19.164.53" rusmininfo.com [30/Apr/2014:11:09:55 +0100] "GET /cron.php HTTP/1.1" 200 5 82 357 "-" "iCabPro" 8.483 "-"
"134.19.164.53" rusmininfo.com [30/Apr/2014:11:09:55 +0100] "GET /cron.php HTTP/1.1" 200 5 82 357 "-" "iCabPro" 11.909 "-"

Could you assist please, I'm at my wit's end trying to figure out what could possibly be wrong.