When applying transitions/deflicker, this happens...
[Image: http://i.imgur.com/quqG6.png]

this is what the image(s) look like before applying lr timelapse.
[Image: http://i.imgur.com/uDGBC.png]

There seems to be a problem when reading the previews of the last images of your sequence. From the screenshot I can't tell more, sorry. Try removing that images from the sequence and try if it works.