Andrew is correct, 'mbralign --help' should show the version. The latest version is 1.40090416.
The first thing you'll want to do is grab the latest version of mbralign (if you don't have it). If this doesn't clear up the problem, we can make arrangements to get the debug output from you.
Here is a description of what is going on:
When mbralign detects a partition that contains an NTFS filesystem (partition type 0x07), it makes adjustments to the NTFS boot sector of that filesystem. A second copy of this metadata is kept in the last 512 bytes of the filesystem as a backup. This backup was very important in the days of physical disk systems because a single sector error (at the right location) could render the filesystem unusable for boot. Today, this is less important especially in the case of a virtual hard drive (vmdk file) on a enterprise storage array.
Both versions of mbralign read the backup boot sector before making adjustments to it. In mbralign 1.2, if the backup didn't match the original, the warning/error you received is displayed. The 1.40090416 version handles this better in that it compares the backup to the original backup (not the original). If it doesn't match in this case (much lower likelihood), you'd get the error as well. In this case, the debug information (--debug) can be used to determine if its safe to use the resulting file.