Hello!
The problem could be solved now:
After deactivating the "Message-Signaled Interrupts" of the "passthroughed" PCI card in the virtual machine, the USB 3.0 controller works now.
This can be done with adding the parameter 'pciPassthru<no>.msiEnabled = "FALSE" ' to the VM configuration.
Following technical note was helpful in this case: http://www.vmware.com/pdf/vsp_4_vmdirectpath_host.pdf.
Thanks.