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I'm having this bootflag issue, too. I had the official Alpha 3 running fine. When I tried to install a nightly build to get the RAW module working, things went awry. When I turn it on, it soon announces the loading of the bootflag along with a smile. The firmware reads as 1.1.3-ml-v2.3.NEXT. When I hit the Trash button, no Magic Lantern menus come up.

I wouldn't mine not being able to uninstall the flag, if Magic Lantern was working, but it's not.

Anyone out there who has this bootflag issue, but has Magic Lantern working?


UPDATE: I kept fiddling (worried about bricking camera with each step), but finally got everything working.
Steps I took:
1) I deleted all the ML files from the SD card. and replaced them with the official 5diii alpha build files.
2) I started up the 5diii with the Alpha 3 on the SD card. The Alpha 3 ML started working again on the 5diii.
3) Then I copied Canon firmware 1.1.3 onto the SD card. I was able to 'update' the 5diii firmware to 1.1.3. (i don't remember every step in that or if there were any issues).
4) then i carefully followed the guide at planet5D -- http://www.cinema5d.com/news/?p=17898
5) and it worked. the bootflag issue disappeared!

CONCLUSION: I think tried to simply update the Alpha 3 to the latest build. Maybe this is what's been happening to others. Good luck!!

Regarding...
"Alex made a replacement autoexec hack that got it going...not able to do Bulb tho."

Would yours even turn on?
Mine does nothing.

After five days of time lapse of artists painting a commissioned mural, the Canon didn't start up the next morning. It seems to be bricked. I've tried all the recommended procedures. No luck. Gonna send it back to Canon.

Anyone have experience sending broken cameras to Canon that have Magic Lantern installed?