The issue in this case is likely, that the custom megaraid-sas vib - required for your RAID controller - is replaced by the update:
2015-03-20T11:37:40Z esxupdate: imageprofile: DEBUG: VIB LSI_bootbank_scsi-megaraid-sas_6.606.06.00-1OEM.500.0.0.472560 is being removed from ImageProfile ESXi-Customizer
2015-03-20T11:37:40Z esxupdate: imageprofile: INFO: Adding VIB VMware_bootbank_misc-drivers_5.5.0-2.54.2403361 to ImageProfile ESXi-Customizer
What you need to do is to ensure that either the driver is not replaced (i.e. only install the required vibs, which might be difficult), or - after installing the patch, and before rebooting the host - replace the megaraid-sas driver again with the required one.
The latest driver can e found at https://my.vmware.com/web/vmware/details?downloadGroup=DT-ESXI55-LSI-SCSI-MEGARAID-SAS-66081100-1OEM&productId=353
André