Apple recovery partition possibly creating problems in Ubuntu
OS X creates the recovery partition as an alternate boot solution for ease of reinstallation and troubleshooting.

It is not needed for normal operation, and as someone that's familiar with boot technology and options, the simplest option would be to simply delete the partition entirely and patch the partition table if needed.

Here is a stock layout:

Mac:~ me$ diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *251.0 GB   disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:                  Apple_HFS Macintosh HD            250.1 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3


You could merge partitions disk0s3 into the partition that precedes it (in this case) to effectively erase and then delete the Apple_Boot partition listed as Recovery HD. In this case, you would need to be booted to some other drive than disk0 to have both disk0s2 and disk0s3 unmountable (which would make them disk1 or higher in all likelihood).

 diskutil mergePartitions JHFS+ "Macintosh HD" disk0s2 disk0s3


Should that not work, you might have to image Macintosh HD to another drive as an img file (or straight partition to partition) and then repartition hdisk0 to have just one partition and restore.



As to the deeper question, my guess is that the "hiding" of the partition isn't compatible with other non Apple tools and is confusing the issue - hence the advice to just remove it and count on alternate options to restore your system or boot externally in stead of the recovery HD.