For those who encountered the same weird networking problems as I did, I was just browsing through the Knowledge Base articles for the patches released yesterday and found out that they fixed the driver for the Intel quad-port nic. When using VST half of the packets were dropped, for more info on the problem check these blogs: 1 , 2.
Fixed ESX Server support for Intel Zoar NICs on a VLAN trunking configuration. A flaw existed between the ESX Server networking subsystem and the igb driver.