What is the exact nature of the error? Does it come from Hyper-V, or is it inside the guest OS? What are the steps that you must take before the VM will boot (that is assuming you are able to eventually get it to boot)?
The cmdlet does modify the NTFS boot sector and NTFS boot sector mirror for NTFS partitions that are bootable. It does *not* modify the Boot Configuration Data (introduced with Windows Vista/Server 2008), which is why a rebuild of the BCD is necessary before a Windows 2008R2 Core guest will boot. A Windows 2003 guest should boot successfully after the alignment without any further modification.