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For what it's worth I just discovered this script and have gone back through my old time lapses and been throwing them at the script.   The stuff I shot in simple AV mode time lapse seems to be a lot better than the stuff I shot  via ETTR time lapse.

I'm still trying to wrap my head around the ETTR Time lapse.  But for me my problems seemed to be around time lapse day to night and ISO changes...  the pictures would keep getting brighter and brighter in ETTR mode and the ISO values would start climbing..

To be clear here... what I'm trying to suggest is that if you are doing ETTR timelapse and throw the results at the the deflicker /ramp script I would suggest the following:

Start with AV mode.  It's a tried and tested method of shooting timelapse with a SLR and for the most part your only problem is flicker.  Shoot a good 3 or 4 hours of 30 sec interval captures and shoot it with sunset right in the middle of the timeline.

Then bring those captures to ACR and the deflicker script. This is exactly what I'm doing right now.   I took 3 cameras out tonight.  A GoPro (just because I can)... a Canon 350D shooting raw in AV mode with intervolmeter and the 5dmark3 shooting ETTR with ML.  I can tell you my 5dMK3 stuff is just a hot mess and I'm pretty sure its my fault.   But the 350D stuff deflickers real nice in ACR with the script.    This might be a good starting place for you to figure out where the problems are.

Well at this point I've done a ML reset due to other issues I was having (probably self inflicted) and its been 2 weeks.   So I'm going to start over and reshoot the location.
I'll knock it down to the smallest raw files I can get and try to recreate all the other settings  (I followed the tutorial as best as I could) .  I will document everything (settings and steps) and then isolate the pairs of frames where the big jumps in exposure occur.

Is there anything else other than settings, ML version and pairs of CR2/XMP + jpg output you would need from me?

Ok do you want certain files from a certain point in the timeline?  In the video link I posted the problem occurs at various intervals where there is a big jump in the footage...

http://www.isaacgolding.com/eagle/ettr-timelapse.zip  the files you requested.

So I've been trying out the MagicLantern on my 5dmarkIII and the last feature I was testing out is ETTR for time lapse purpose.
Ive been able to create Time lapse videos from ETTR but there were problems with flicker.

Enter ETTR timelapse flicker free directions.  http://www.magiclantern.fm/forum/index.php?topic=5705.0

I followed the instructions judiciously and at this point this is my end result:  http://youtu.be/mszT2KXQLA8

At this point I'm open to suggestions.  I'm not sure where to go but at this point ETTR time-lapse "flicker free" isn't working out well for me.

So I'm still struggling to really nail down ETTR timelapse with post deflicker using XMP ACR via Bridge in Mac.

I went to a very nice vista and pointed my camera into the sun over a scene and followed the ETTR tutorial with setup for XMP.  I processed via the directions for XMP Bridge and ACR and then assembled the pictures using GoPro's video software (which does a great job of converting jpg timelapse into video)

Here is the end result.
http://youtu.be/mszT2KXQLA8

I'd love some suggestions and I can make a zip with the original 300 some pics available if somebody wants to look at those settings.

I hate to say it, but Ive read over the whole thread a couple times and to be honest I'm still confused about the work flow.

I've been trying the XMP workflow with Bridge CC2014 on the Mac  (bridge 6.1.blah) and I'm missing a step or adding a step because I end up with a lot more flickr.

I'd love to see an updated workflow for the XMP/Bridge method of deflicker