Why every security update touches partitions and boot loader

Hi everyone,

I have noticed that each time I get a system update (e.g. security update) my boot loader (Refind) gets overwritten and the partitions assigned to the protective MBR (so the ones visible by Windows in bootcamp) are replaced with the ones decided my OS X. This is very frustrating because each time I have to use gdisk to fix this. Is there any way to prevent this?

This is the GUID partition table:

Number  Start (sector)    End (sector)  Size       Code  Name
   1              40          409639   200.0 MiB   EF00  EFI System Partition
   2          409640      1952528607   930.8 GiB   AF00  MAC OS X
   3      1952528608      1953798143   619.9 MiB   AB00  Recovery HD
   4      1953798144      3897692159   926.9 GiB   0700  Basic data partition
   5      3897692160      5860270079   935.8 GiB   0700  DATI

This is my protective MBR:

Number  Boot  Start Sector   End Sector   Status      Code
   1                     1           39   primary     0xEE
   2                    40       409639   primary     0xEF
   3      *     1953798144   3897692159   primary     0x07
   4            3897692160   5860270079   primary     0x07

This is the one written by OS X after update:

Number  Boot  Start Sector   End Sector   Status      Code
   1                     1       409639   primary     0xEE
   2                409640   1952528607   primary     0xAF
   3            1952528608   1953798143   primary     0xAB
   4      *     1953798144   3897692159   primary     0x0C