I am having the same issue on a new install of Debian Wheezy. The disk
has been partitioned using the partitioning tool during the install. 

    yann-laptop# parted /dev/sda "unit B p"
    Model: ATA WDC WD2500BEVT-8 (scsi)
    Disk /dev/sda: 250059350016B
    Sector size (logical/physical): 512B/512B
    Partition Table: msdos
     
    Number  Start          End            Size          Type      File
    system  Flags
     1      1048576B       299892735B     298844160B    primary   ext3  
           boot
     3      300940288B     70299680767B   69998740480B  extended
     6      300941312B     30300700671B   29999759360B  logical   btrfs
     5      30300700672B   70299680767B   39998980096B  logical
     2      246058844160B  250059161599B  4000317440B   primary
     
    yann-laptop# parted /dev/sda "unit CHS p"
    Model: ATA WDC WD2500BEVT-8 (scsi)
    Disk /dev/sda: 30401,80,62
    Sector size (logical/physical): 512B/512B
    BIOS cylinder,head,sector geometry: 30401,255,63.  Each cylinder is
    8225kB.
    Partition Table: msdos
     
    Number  Start         End          Type      File system  Flags
     1      0,32,32       36,117,16    primary   ext3         boot
     3      36,149,47     8546,199,36  extended
     6      36,149,49     3683,216,52  logical   btrfs
     5      3683,216,53   8546,199,36  logical
     2      29914,242,24  30401,75,9   primary
     
     
    yann-laptop# cfdisk /dev/sda
    FATAL ERROR: Bad logical partition 6: enlarged logical partitions
    overlap
    Press any key to exit cfdisk 

I can't see any error in the table partition showed by parted, yet
cfdisk is complaining about partition 6.

Further investigating the issue, I noticed (using apt-file) that
/sbin/cfdisk is provided by two different packages that seem to be
overlapping: util-linux, which provides the tool available by default,
and gnu-cfdisk,that seems to be overwriting the existing  /sbin/cfdisk
when installed (at least /sbin/cfdisk is not a symlink and there is no
such reference in /etc/alternatives).

Please note that the /sbin/cfdisk provided by gnu-cfdisk works fine in
my case.

Regards,
Yann



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