Disk utility repair doesn't repair os disk

Disk utility (13) keeps saying
Invalid B-tree node size
The volume  could not be verified completely.
and, once it has shown "updating boot support partitions for the volume as required", says "This disk needs to be repaired. Click Repair Disk."
But I'm getting the impression that clicking repair disk does not help - even after about ten times, the messages stay the same.
I can't re-partition the disk as all those options are grey, even though I'm booted from an external USB drive.
The machine is a MacPro, early 2009, OS X 10.9.3 (13D65), disk is encrypted journaled HFS+, used to have a Bootcamp partition a few years ago but is now a single partition.
I can probably no longer boot from this drive, each time takes longer and last time took almost thirty minutes, so I'm really looking of a good fix.
Any suggestions?
Regards,
Bob

Eric,
I've first tried Disk Utility when booted from the Recovery of the disk itself. Didn't help and also didn't offer a re-format option.
I've then made a USB bootable, booted from that and tried Disk Utility - didn't help.
I've then booted from the Recovery of the USB and tried Disk Utility - didn't help.
I've since used diskutil reformat on the command line and found to my surprise that the disk is now empty but the "Invalid B-tree node size" remains.
It seems reformatting does not reset the indexes of the disk
And every now and then I still see a remark about the "Windows boot.ini files" - which I also wouldn't expect after reformatting.

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