Wow, Christopher Murphy, you are extremely generous and helpful with your time and advice throughout this thread. I'm amazed by the willingness to help strangers you've never met.
I hope you may be willing to spend some time helping me as well. I've got somewhat of a unique situation (I believe).
I have a 13" Macbook Pro 9,2 (mid-2012). It came with a 750gb SATA HDD and internal optical drive. I installed a Samsung 840 Pro 256gb SSD in place of the HDD, then put the HDD in place of the optical drive. I have the system set up so that the SSD is my primary OSX drive with one single visible partition. Then I have the HDD set up so that the first 500gb is an HFS partition, and the rest is set aside for bootcamp. It was originally one 750gb single HFS partition, but then I used the boot camp assistant to section off the last 250gb for windows.
For the life of me I couldn't get a bootcamp install to work off of a Boot Camp Assistant created a x64 Win7 USB stick, until I read somewhere that I needed to actually disconnect the sata connector for my SSD. This worked, and Win7 was able to format from FAT32 to NTFS, then install and boot correctly from the HDD (with the SSD unplugged), and leave the HFS 500gb partition intact.
Then when I plugged back in the SSD, OSX can see that there is a bootable partition when I go in to "Choose Startup Disk" in SysPrefs, and if I hit the option key while booting, but all I get is a black screen with a blinking cursor. I believe that x64 Win7 is mad at me because I have changed the drive numbers that it uses to references how to boot up properly. I believe the solution may lay in running a Win7 boot repair set of commands, but I can't seem to access the Win 7 recovery console or "Repair Installation" feature using the USB stick that BCA created.
To complicate matters further, I successfully created a Ubuntu 13.04 USB stick, used rEFIt to boot off of it, and then had it split off and use the second half of my 250gb ntfs partition on the HDD to install linux.
To complicate things even further, I am using filevault2 with FIPS encryption module to encrypt both the SSD, and the HFS partition on the HDD.
I have installed rEFIt and used "bless" to have it be my boot selection menu (as instructed here: https://wiki.debian.org/InstallingDebianOn/Apple/MacBookAir/2-1#EFI_and_Partitio ning). I can boot successfully into OSX, and I can boot successfully into Ubuntu. I still can't boot into Win7 though.
Here is the output from a variety of commands I've seen you ask others for: (http://pastebin.com/u3V01iWR)
mbltccmbp:~ trevorcobb$ diskutil list
/dev/disk0
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *750.2 GB disk0
1: EFI 209.7 MB disk0s1
2: Apple_CoreStorage 501.8 GB disk0s2
3: Apple_Boot Boot OS X 134.2 MB disk0s3
4: Microsoft Basic Data BOOTCAMP 124.0 GB disk0s4
5: Microsoft Basic Data 115.5 GB disk0s5
6: Linux Swap 8.5 GB disk0s6
/dev/disk1
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *250.1 GB disk1
1: EFI 209.7 MB disk1s1
2: Apple_CoreStorage 249.2 GB disk1s2
3: Apple_Boot Recovery HD 650.0 MB disk1s3
/dev/disk2
#: TYPE NAME SIZE IDENTIFIER
0: Apple_HFS Macintosh SSD *248.9 GB disk2
/dev/disk3
#: TYPE NAME SIZE IDENTIFIER
0: FDisk_partition_scheme *8.3 GB disk3
1: DOS_FAT_32 WININSTALL 8.3 GB disk3s1
/dev/disk4
#: TYPE NAME SIZE IDENTIFIER
0: Apple_HFS Macintosh HD *501.5 GB disk4
mbltccmbp:~ trevorcobb$ sudo gpt -r -v show disk0
Password:
gpt show: disk0: mediasize=750156374016; sectorsize=512; blocks=1465149168
gpt show: disk0: Suspicious MBR at sector 0
start size index contents
0 1 MBR
1 1 Pri GPT header
2 32 Pri GPT table
34 6
40 409600 1 GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
409640 980102336 2 GPT part - 53746F72-6167-11AA-AA11-00306543ECAC
980511976 262144 3 GPT part - 426F6F74-0000-11AA-AA11-00306543ECAC
980774120 792
980774912 242186240 4 GPT part - EBD0A0A2-B9E5-4433-87C0-68B6B72699C7
1222961152 225603584 5 GPT part - EBD0A0A2-B9E5-4433-87C0-68B6B72699C7
1448564736 16582656 6 GPT part - 0657FD6D-A4AB-43C4-84E5-0933C84B4F4F
1465147392 1743
1465149135 32 Sec GPT table
1465149167 1 Sec GPT header
mbltccmbp:~ trevorcobb$ sudo gpt -r -v show disk1
gpt show: disk1: mediasize=250059350016; sectorsize=512; blocks=488397168
start size index contents
0 1 PMBR
1 1 Pri GPT header
2 32 Pri GPT table
34 6
40 409600 1 GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
409640 486717952 2 GPT part - 53746F72-6167-11AA-AA11-00306543ECAC
487127592 1269536 3 GPT part - 426F6F74-0000-11AA-AA11-00306543ECAC
488397128 7
488397135 32 Sec GPT table
488397167 1 Sec GPT header
mbltccmbp:~ trevorcobb$ sudo fdisk /dev/disk0
Disk: /dev/disk0 geometry: 91201/255/63 [1465149168 sectors]
Signature: 0xAA55
Starting Ending
#: id cyl hd sec - cyl hd sec [ start - size]
------------------------------------------------------------------------
1: EE 0 0 1 - 1023 254 63 [ 1 - 409639] <Unknown ID>
2: DA 25 127 15 - 1023 254 63 [ 409640 - 980102336] <Unknown ID>
3: AF 1023 254 63 - 1023 254 63 [ 980511976 - 262144] HFS+
*4: 07 1023 254 63 - 1023 254 63 [ 980774912 - 242186240] HPFS/QNX/AUX
mbltccmbp:~ trevorcobb$ sudo fdisk /dev/disk1
Disk: /dev/disk1 geometry: 30401/255/63 [488397168 sectors]
Signature: 0xAA55
Starting Ending
#: id cyl hd sec - cyl hd sec [ start - size]
------------------------------------------------------------------------
1: EE 1023 254 63 - 1023 254 63 [ 1 - 488397167] <Unknown ID>
2: 00 0 0 0 - 0 0 0 [ 0 - 0] unused
3: 00 0 0 0 - 0 0 0 [ 0 - 0] unused
4: 00 0 0 0 - 0 0 0 [ 0 - 0] unused