I was having the same issue. But this is what I did to fix it. Kind of a lot of work!
I think the problem was my Hboot was at 1.57 and that messed with all the RUUs. I tried several different ones and that explorer failed every time. Once I put it on Hboot 1.44 and ran the 1.29RUU it worked on the first try.
1. S-Off your device (if not already!)
2. Download the Hex Stock Zip from here: http://forum.xda-developers.com/show....php?t=2314921
3. Download the Bootloader Unlock Tool from here: http://www.htc1guru.com/2013/11/new-...r-unlock-tool/
4. Download this RUU (it can only be this one!!): http://forum.xda-developers.com/show....php?t=2250904
5. Once you're s-off, transfer the Hex Stock Zip to your device and flash it in TWRP (or whatever custom recovery). This should make your bootloader show HBoot 1.44 again.
6. Transfer the Bootloader Unlock Tool to your device and flash it in recovery. You'll want to check the option to lock your bootloader.
7. Connect your phone to the USB and run the RUU wizard. This should take about 10 minutes but it should work! (It didn't look like it was working for me at first, but eventually I could see the progress bar on the phone moving.)
8. Next, you'll have to boot back into fastboot and "fastboot oem writesecureflag 3" to turn s-on.
9. The phone will be running Android 4.1 (I think), so you'll have to update it about 5 times before it's on Sense 6.
Hope this works!!