Win 8.1 Upgrade causes GPT/MBR Mismatch

Question

I am responsible for 9 Mac minis (late 2012) in a computer training lab. I set them up last summer to dual boot Windows 8 Pro using Boot Camp. Recently, I tried upgrading one of the minis to Windows 8.1. The upgrade downloaded from the Microsoft Store and installed with no issues. Or, so I thought. Everything continued to work as before and I had no problem booting back and forth between the two operating systems. It wasn't until I attempted to make a disk image backup of the computer using Clonezilla that I discovered there was a problem. Clonezilla displayed the error message "This disk contains mismatched GPT and MBR partition" and would not do the backup. Thus began a lengthy journey of discovery about MBR, GPT, gdisk, etc.
So, here's what happened. The Windows 8.1 upgrade automatically (with no input whatsoever from me) resized the BOOTCAMP partition to be about 350MB smaller than it was previously. I have no idea why it did this and I haven't been able to find any report of this anywhere on the internet. Anyway, in resizing the partition, Win 8.1 of course modified the MBR partition table. However, it did not modify the corresponding partition information in the GPT partition table.
I was able to fix this using gdisk to delete the GPT BOOTCAMP partion info and recreate it using the correct first and last sector numbers from the MBR partition table. This procedure is described in detail in this forum and other places on the internet. So, I'm good to go. But, I'm posting this here because I haven't seen any report of this issue anywhere else. If you have upgraded a previously installed BOOTCAMP partition to Windows 8.1, I strongly urge you to get gdisk (download at http://sourceforge.net/projects/gptfdisk) and run the verify (v) command to verify whether you have this issue. You can also verify by running
sudo gpt -r -vv show disk0.
Mark Ulmer

Answer 1

Yes. First, download gdisk (URL in the OP) and run the installer package. Then run gdisk from a terminal window and run the v (verify command). If verify indicates no problems, then you're good to go and can just type "q" to quit. However, if it shows something like this, then you have the problem:
sudo gdisk /dev/disk0
Command (? for help): v
Warning! Mismatched GPT and MBR partition! MBR partition 4, of type 0x07, has no corresponding GPT partition! You may continue, but this condition might cause data loss in the future!
Identified 1 problems!
Next, display the MBR partition table and make note of the start and end sectors for your BOOTCAMP partition. This should be partition 4 unless you've added additional partition(s), which is not officially supported by Boot Camp. It should show something like this:
Command (? for help): r
Recovery/transformation command (? for help): o
Disk size is 1953525168 sectors (931.5 GiB)
MBR disk identifier: 0x7C170CB2
MBR partitions:
Number  Boot  Start Sector   End Sector   Status      Code
   1                     1       409639   primary     0xEE
   2                409640    975693095   primary     0xAF
   3             975693096    976962631   primary     0xAB
   4      *      976963584   1952806911   primary     0x07
Next, display the GPT partition table information. Compare the start and end sectors for partition 4 to the MBR partition 4 start and end sectors. Most likely the start sectors will match, but the end sectors will be different.
Recovery/transformation command (? for help): m
Command (? for help): p
Number  Start (sector)    End (sector)  Size       Code  Name
   1              40          409639   200.0 MiB   EF00  EFI System Partition
   2          409640       975693095   465.1 GiB   AF00  Customer
   3       975693096       976962631   619.9 MiB   AB00  Recovery HD
   4       976963584      1953523711   465.7 GiB   0700  BOOTCAMP
Next, delete the GPT partition 4. (Note: this does not delete the actual partition from disk. It only deletes gdisk's in-memory representation of the GPT).
Command (? for help): d
Partition number (1-4): 4
Now, create a new partition 4 using the start and end sector values from the MBR partition 4.
Command (? for help): n
Partition number (4-128, default 4): 4
First sector (34-1953525134, default = 976962632) or {+-}size{KMGTP}: 976963584
Last sector (976963584-1953525134, default = 1953525134) or {+-}size{KMGTP}: 1952806911
Current type is 'Apple HFS/HFS+'
Hex code or GUID (L to show codes, Enter = AF00): 0700
Changed type of partition to 'Microsoft basic data'
Now, change the name of the new partition 4 to BOOTCAMP:
Command (? for help): c
Partition number (1-4): 4
Enter name: BOOTCAMP
Run the verify command. It should report no problems. If it still reports a problem, quit (q command) and start over.
Command (? for help): v
If everything checks out, write new partition table to disk and exit.
Command (? for help): w
Reboot and test your dual boot setup to verify all is working correctly.