What type of virtual disk controller did you select in the conversion wizard? For Windows 2003 the "LSI Logic Parallel" controller is the default.
Depending on the target virtual disk type it might be possible to modify the controller type to avoid another conversion. In case there's a small .vmdk file (a text file with a few hundred bytes in size), compress/zip this .vmdk file along with the VM's .vmx file and attach the .zip file to your reply post to see what can be done.
André