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I shot them in RAW, that was after just a little bit of fiddling with Lightroom. The settings I used were ISO 100, F/9.0, 8 second exposure. I shot it using a Tokina F/2.8 28mm-70mm at 28mm mounted on my 600D with a tripod of course. The shot was actually pretty over exposed - thank goodness I had taken it in RAW. I had left the camera out unattended like I said and as the sun was coming up it brought a lot of extra light which almost made many shots unusable.

I live in northern CA where lightning storms usually just stick to being in the mountains away from civilization. Last night however there was a series of storms that came through and blasted us with lightning from 2 in the morning to 6 in the morning. I didn't manage to do a decent time lapse of the event but I did get some pretty great shots thanks to the intervalometer feature! I uploaded them to my Google Drive account and it doesn't support embedding and I didn't want to have to re-upload the enormous files so I just picked out my favorite as a 'thumbnail' and hosted it somewhere else to embed it. Enjoy the full album here: https://drive.google.com/folderview?id=0BzX3H2-eZ6FWM29ZX1J6UXhkd0E&usp=sharing

I have had this same issue with my 600D. Don't keep using the card until you get your pictures off it! The pictures 'are' there! What I had to to do was use a recovery software while reading the card with an SD reader and not through the camera. Personally the software I used was Recuva. The crazy part is you may need to do a quick format on the card first before the recovery software can actually find the missing pictures, it's really odd. On Recuva I set it to do a deep scan and search the entire card after a quick format. I tried using the software before formatting the card and it only found a few pictures from other times I had used the card. Personally this software is a must for anyone! I managed to find all the pictures from a timelapse I had taken (16 second shutter time with ML intervalometer set to take pics like crazy with no limit) but they were all named the same thing: My name. Kinda creepy I thought at first until I realized I had put my name in the copyright section of the camera. I really hope you haven't used this card since then and you can get those pictures back. I was just searching for an answer to this problem too since I took a timelapse last night with a fresh card and fresh ML install and it did it to me again. I actually haven't had time to try and recover the latest batch of pics but I will do so later today and check back here with my results. It's a huge hassle if I have to recover the pictures every time I want to do a timelapse!