If you use a USBPorts kext previously created with a different SMBIOS, yes, that's perfectly normal. Why? Because your mapping of USB ports no longer matches what you created.
So you either:
1) revert to MBP11,x SMBIOS you previously used and add boot arg -no_compat_check
or:
2) re-create your USBPorts kext with hackintool.
Try replacing with these files
Add patches for Fn key for Brightness
Add patches to disable unused ports, known to cause lag if you have i3 cpu
Add patch to enable VGA, may or may not work
E5540_Fixes.zip