In the meanwhile here are some wild guesses:
- Check the disk for corruption (e.g. 'chkdsk /f /r /b'). Fragmentation is not known to cause issues with P2V, while corruption does. Perhaps you have already done that. If not, please do.
- Almost certainly not the case, but... SQL server supports databases on raw disks (unformatted). In this case the partitions on the source machine will also have no NTFS.
- Converter makes a VSS snapshot of the source and then reads from it. Look for any VSS related issues (in converter agent log, in event viewer, in SQL server logs perhaps(?)
- I suppose the conversion uses block level cloning (as opposed to file level) because if file level, converter formats the destination partitions. Block level is default unless you shrink an NTFS volume or change its cluster size or resize a FAT volume.