I first set the camera to manual and set it to take 3 shots each time at varying exposures (-2, 0 and +2). Then i set the interval which varied depending on the situation. I used photomatix to create the HDR photos, then lightroom to resize the images, then lrtimelapse to deflicker. The photos were then exported from lightroom and then I used quicktime 7 to combine the photos. The resulting videos were edited in Final cut pro.
I did also edit the photos in lightroom a bit, but i didn't want to edit them to drastically as lightroom works destructively, thats why I wanted to use an HDR method as it would allow me to bring out all the colour available while not damaging image quality. I tried to keep the clips as realistic as possible but some im not overly happy with.
As for the bugs, I agree they are a bit annoying but there wasn't much i could do about them.
Thanks for all the feedback its all really useful, keep it coming...