do diskutil list from Terminal and post the output here. Maybe add a description of what's on each partition and whether it's supposed to be bootable or not.
Last login: Mon Oct 18 18:50:09 on console
Mikes-Mac-Pro:~ mike$ diskutil list
/dev/disk0
#: TYPE NAME SIZE IDENTIFIER
0: FDisk_partition_scheme *122.9 GB disk0
1: Windows_NTFS 122.9 GB disk0s1
/dev/disk1
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *250.1 GB disk1
1: EFI 209.7 MB disk1s1
2: Apple_HFS OSXsl 230.1 GB disk1s2
3: Apple_HFS Backup 19.5 GB disk1s3
/dev/disk2
#: TYPE NAME SIZE IDENTIFIER
0: FDisk_partition_scheme *500.1 GB disk2
1: Windows_NTFS Win7 64bit 500.1 GB disk2s1
/dev/disk3
#: TYPE NAME SIZE IDENTIFIER
0: FDisk_partition_scheme *250.1 GB disk3
1: Windows_NTFS Win7 32bit 138.9 GB disk3s1
2: Linux_Swap 40.0 GB disk3s5
3: Linux 71.1 GB disk3s6
Mikes-Mac-Pro:~ mike$
Disk0 contains Windows XP and shows up but does not boot (Flashing cursor)
Disk1 contains OSX and boots fine
Disk2 contains Windows7 64bit, this shows as an option but boots 32bit
??
Disk3 partition1 contains Windows7 32bit and boots fine
Disk3 partition3 contain Ubuntu but does not show (although it used to before the last format and re-install)
All os were installed with all the other drives disconected and Ubuntu has grub2 on it's /
I have used easybcd on windows 32bit to add all os which will boot all except osx.
Mike