When installing a Debian-based Linux distribution on a system with an extended partition included in the Linux boot item, and using BootIt BM (BIBM) as boot manager with primary partitions not limited, the following warning message appears when BIBM is started up on the first reboot after the installation completes:
Warning: A new or altered primary partition was found on HD0 which may overlap an existing partition! You should use Partition Work to check for errors.
When first entering Partition Work under these conditions, there will typically be two extended partitions visible in the list of partitions. In other words, the right-most column in Partition Work will have two partitions defined as "Extended", where originally (before the Linux install) there was only one. Both extended partitions will be marked with an "E" (for error) in the center column, and the message *Errors Exist* will be visible above the list of partitions. In addition, some or all of the volumes in the extended partition may be listed under both extended partitions, and the names for some of the volumes may be missing.
The installers for Debian-based distributions (Debian, Ubuntu, Kubuntu, Linux Mint, etc.) contain a bug/anomaly where they will unconditionally move the beginning of the extended partition to a position 2 sectors before the beginning of the first logical volume inside the extended partition. This typically will happen regardless of whether or not any actual partition changes are made during the install.
Note that an extended partition will normally begin either 63 or 2048 sectors before the start of the first logical volume in an extended partition, depending on whether the partition table is aligned on 2048 (2k) sector boundaries, or is CHS aligned. This is a generally accepted practice, including by Linux partitioning utilities. It is unknown why this group of Linux installers move the beginning of the extended partition.
For reference, a description of this issue, including the before/after partition tables, is available in the following Debian bug report:
On reboot, after the installation completes, you will need to deal with the issue of having two extended partitions showing in Partition Work. The simplest and least troublesome procedure to correct this situation is outlined below. If this procedure is followed correctly, you should not lose any data, and Linux should be bootable afterwards:
1. In Partition Work, highlight the original extended partition (the one that comes first in the list of partitions - the one on top), select the Delete button, and then confirm the delete. You should now have just one extended partition, and the *Errors Exist* message should be gone.
2. Usually, the remaining extended partition (the new one created by the Linux installer) will have an automatically assigned name such as MBR Entry 1 or MBR Entry 2. If desired, this name can be changed by opening the Properties window for the extended partition and typing in the desired name.
3. Usually, the name for the first logical volume in the extended partition will be blank. A name can be assigned by opening the Properties window for the volume and typing in the desired name.
4. In most cases, deleting the original extended partition (step 1 above) will remove the extended partition from the Linux boot item. To correct this, open the Boot Edit dialog for the Linux boot item, and use the Fill button to insert the remaining extended partition into the desired slot in the MBR Details section of Boot Edit.
To avoid having to deal with this situation at all, there are a few options available, and they are listed below:
1. Use only primary partitions in the Linux boot item.
2. Limit primary partitions in BIBM (problem only occurs if primaries are not limited).
3. If an extended partition exists on the drive for other operating systems, exclude it from the Linux boot item. The installer will not move the extended partition in this case, since it will not be aware of it. If desired, the extended partition can then be inserted into the Linux boot item after the installation completes, with no resulting problems.