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Next things I tried at home:
1, Burn-in test - completed sucesfully after some long test shooting (reached 48C max temperature). No crashes. Interesting find, but I need to repeat it several times.

2, In-camera card benchmark - crashed after while. Temperature was low (cannot remember exactly, but I took camera and started benchmark without any warm-up). It crashed. Now Im suspecting my Komputer Bay 64GB card and will focus on it little bit more. I want to try reformatting it in computer - some useful info I found is here: http://www.magiclantern.fm/forum/index.php?topic=6554.100 ("Aligned + 64K clusters is giving me the best speeds.. expect a 1-2mb cut from formatting in camera to 32k clusters. At least on 64GB cards.")

Can this be overheating issue?

Done more testing yesterday at home (indoor). Formated card (64 GB 1000x Komputer Bay), started recording in full sensor mode and let it record almost full card in few long takes. No problem at all. Temperature started at about 30C, quickly raised to about 40C and stayed here. No frame skipping issues or crashing. Now Im little confused. Maybe higher outside temperature (on sun) plays some role here. Will keep trying outside and watching temperature carefully. I hate to discuss with myself, but hopefully my findings may help someone else in the future :-D

I still experience crashes on latest nightly build. See my Reply #42 on: April 10, 2014, 08:24:32 AM. Today it happened two times (filmed near full 64GB card). Im now turning frame skipping ON (as it crashes just AFTER first frame skip) and fps from 23.976 to 24. Tommorow I will try it another day to see if changed settings make some difference. Any better ideas?

Still same. But now it most of the times only skips frames and does not crashes. Can anyone help me or do I have to stop bothering you guys? Maybe Im missing something important. I do not know, Im new to the whole ML thing...

Can this be overheating issue?

Cons:  It is with great disappointment though that I have to report that despite the incredible image quality the 50D captures, overheating seems to be a major issue.  Production flow was halted multiple times by frame skipping and camera freezing up.  Even turning the camera off in between takes for a few minutes had minimal effect in preventing the sensor from getting hot quickly again. 

Thank you for your detailed experience. Seems like I found source of my problems --> overheating

I still experience crashes on latest nightly build. See my Reply #42 on: April 10, 2014, 08:24:32 AM. Today it happened two times (filmed near full 64GB card). Im now turning frame skipping ON (as it crashes just AFTER first frame skip) and fps from 23.976 to 24. Tommorow I will try it another day to see if changed settings make some difference. Any better ideas?

Once I will have it in my hands I will make some test footage in the city (tried that couple of weeks ago but most of full sensor shots was unusable due to excessive aliasing and moiré). Now I only hope it will arrive soon...

Just want to say the 50D is well worth the continued magic lantern updates until perfection is attained.  I recently acquired a Mosiac Engineering VAF-50D Optical Anti Aliasing filter and did some test footage with it.  Needless to say I am very happy with the results and quality. 

Your footage shows it! It is even better than what I expected! 50D + VAF is killer combination. I cannot wait longer for my VAF filter - just ordered it few days ago ;o)

Here is what I got last weekend - shot mostly in full sensor without VAF: https://vimeo.com/91965491
Using Cineform RAW workflow to Adobe Premiere - that is pretty awesome too

[RAW]

The 1st time I tried to record it lasted just about a minute and then the camera reported 1 skipped frame and locked up, so I had to remove the battery.  After that it recorded for 5 minutes straight with no issues whatsoever. 

I have same problem on my 50D. Right now Im on nightly from 22.3. and it was same on older build from beginning of March. I will try it again on latest nightly build soon and report back.
I get those "1 skipped frame lock-ups" very often. About 1/4 of all cases and it is very annoying as you must turn it of, remove battery, turn on (then it skips modules) so you have to turn off again and then on. Now I have next try ) Sometimes problem repeats couple of times. This drives not only me, but even my unpatient wife very CRAZY :-)
Scenario is always the same. I start recording. 50D starts record session and displays indicator on screen. Now it either continues smoothly without any problem, OR it indicates 1 skipped frame and immediately crashes. Now you are not able to stop recording or do anything else... RAW file is not saved. This happens in both full sensor mode and in crop mode.

Im set like this:
This is RAW Rec on
1568x882 
Global Draw on all modes
Zebras on
Spotmeter off
Waveform off
FPS Override on 23.976 (tried both Exact FPS and optimize for Low Light)
Expo. Sim on
File Manager on
RAW Play on

Using Komputerbay 64 GB 1000x card

So now we know that problem is in both MLV and in RAW recorder. What I want to try (if this will still happen on latest build) is to set frame skipping to be allowed. Now I have it set to stop on skip.

Let me know if you need any further info or something to try... I will update in next few days.