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Latest nightly builds have a new installer. There were issues with "old" installer and deinstallation on 650D.
Format card in cardreader, format card in cam. Then upgrade to Canon firmware 1.0.4.
Format card again in cam and copy extracted nightly build contents to card.
Run firmware update again and wait until timeout sets in.

Sorry, my wrong. Yes, it's MLV_REC.mo, of course.

Modules tab. MLV_RAW.mo has to be loaded.

Sidenote: 5D3's SD-card interface is limited to about 21 MByte/s writing.

Okay! Where can I find the Alpha5b Version?

http://www.filedropper.com/magiclantern-nightly2015apr2170d111a
http://www.filedropper.com/magiclantern-nightly2015apr2370d111b

I never heard about incompatible CF cards and the problem you are describing is not ML related.
Use h2testw or F3 to test card's integrity and get a decent cardreader. I use Kingston FCR-HS3. Others will do as well. See http://www.cameramemoryspeed.com/reviews/card-readers/
Maybe your cardreader just needs a firmware update, if any.

You *are* using a nightly build ...

I don't know what you mean by "installing modules". Did you mean setting all modules to ON?

Nah, take your time and some coffee.

? Modules for zebras and focus peak?

I'm surprised! RAW video is not implemented in v2.3 and you did it anyway.

How do you came to this conclusion? Posts above indicate a solution.

Modules tab -> MLV_REC.mo

Modules tab.

Apples and oranges.

Sorry, this is RAW and doesn't contain any metadata. I have no idea which settings you used (I asked before). Either provide proper info or send MLV.

Good point!
Leroy, use h2testw on Windows to verify card's integrity.

Dual ISO?

H.264 or RAW/MLV? Which settings?
You may upload some unprocessed files somewhere and link them here.

You may want to use search first.

Wait before card removal *after* opening card compartment door. See http://wiki.magiclantern.fm/install

HDR video has to flicker because it will use alternating exposure settings. Remove flicker in post-processing: http://www.magiclantern.fm/forum/index.php?board=14.0

Again: All SD-to-CF adapters I know/heard of are not worth a dime. Performance is crap and compatibility, too.

Any way you like.
And SD-to-CF adapters are known for compatibility problems. Get rid of it.

Have you tried the solution offered in first reply?