Disk Utility - Partition map needs repair because a data partition needs loader space.

I just finished setting up both my OSX and Windows installs from scratch after fitting an SSD, which in-turn was right before my logic board died and Apple replaced it, now it looks like I have some sort of hard drive issue brewing.
This was my plan for the SSD, and how it currently displays in Disk Utility although that wasn't the case earlier:
And in Terminal:
My intention was to have two boot partitions for each OS, 'Macintosh HD' and 'Win 7 Pro' and a third shared data partition 'Projects' on the SSD, which I made in Drive Genius after installing Boot Camp. I don't want Macintosh HD accessible from Windows because I'll be using Paragon HFS+ or MacDrive to give write access and don't want OSs stomping on other OSs turf, hence needing three partitions. Everything looked fine until I just checked Disk Management under windows and realised it couldn't see the Projects volume. Even though it's fine in OS X, it was just marked black/unallocated space.
So I booted back into OSX, all my files look fine so I ran Disk Utility and the Partition tab looked really odd - unfortunately I didn't get a screenshot. All volumes reported their size correctly but visually, Macintosh HD took up most of the drive. I could see 'Windows 7 Pro' under this, but the Partition Layout section had a scrollbar, which if I scrolled down showed 'Projects' squished into a tiny gap at the bottom. I ran a Verify, which reported no problems, and at some time since the Partition Layout has reverted to how it should look (as in the screenshot above), with 'Projects' book-ended by "Macintosh HD' and 'Windows 7 Pro'.
Now when I run a Verify on Macintosh HD or Projects volumes, it says there's no problem, but if I run one on the drive, I get this message:
Volume Macintosh HD on disk0s2 has 0 bytes of trailing loader space and it needs 134217728 bytes
Problems were found with the partition map which might prevent booting
Error: Partition map needs repair because a data partition needs loader space.
I've only managed to find one other mention of this error here, but the fix is not relevant to me because I don't have Sophos installed. I've tried Single User/Safe Mode but it just boots into normal mode, so I can't do a fsck -fy.
** /dev/rdisk0s2 (NO WRITE)
Can't open /dev/rdisk0s2: Permission denied
That value in bytes is exactly 128mb, so I suspect the problem lies with one of the invisible partitions that show up in iPartition and Disk Management under Windows, but not in Disk Utility. I have backups and I suspect the root of the problem is partitioning in iPartition after installing Boot Camp, but I've never had issues with this approach in the past so I'm wary of just giving up and reinstalling Windows again will be massive hassle because I no longer have a SuperDrive and last time it refused to install from USB.
Anyone have any idea what's going on? It seems like the sort of issue Disk Utility should just handle, at least in Recovery mode, but it's not playing ball. It also doesn't seem like a massive problem since my files all look fine and performance is OK, so I'm reluctant to do anything major.
I'll update with a shot of the drive in Disk Management from Windows in a few minutes, in case that sheds light on anything. Thanks!

Similar issue here. I manually partitioned my hard disk for triple boot (using Gparted on Linux), then everything was just fine until I ran bootcamp, to do something as simple as create a boot USB.
I get the same error as a result and have to work my way into booting, by resorting first to a Linux live USB, then restarting from the live USB, to finally reach my rEFInd boot manager, or whichever boot manager should be initialized at startup.
I suppose that the cause in my case is that some operation "scratched" the protective MBR. See this:
http://www.mactech.com/articles/mactech/Vol.23/23.03/APMtoGPT/index.html
I am hoping to fix it using an external Yosemite installation media: see this guide -
http://www.macworld.com/article/2367748/how-to-make-a-bootable-os-x-10-10-yosemi te-install-drive.html
And as a last resort to reinstall.
I'll admit I am negatively surprised. I need this computer for professional reasons, and for the sake of "preserving the integrity of OSX", measures defined by Apple instead tend to make partitions far easier to damage. And this problem seems to affect a number of users.
As for what I have to go through to fix it: a 5GB download, during which I have to register my credit card to the Apple Store. "Pay first, get your free software next."
IF Disk Utility can fix it, from the external media, then fair enough. The hassle is unpleasant but it files as "a choice".
Otherwise you can file it safely under software design calamity.

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