I have a folder of JPEGs exported from LR after metadata editing with LRTimelapse.
If I render the video with LRTimelapse, the video turns out choppy, with 2 (in this specific case) jumps of many frames, which are clearly visible when playing the video. The whole video is 6 seconds while it is 15 seconds if rendered with a freeware software like Time Lapse Assembler.
Experienced with both LRTimelapse 3.2.1 and 3.3.1 on a new iMac with OSX Mavericks.
Thank you

This is not a bug. Probably it's something with the image sizes/crops. Please check this faq post:
http://forum.lrtimelapse.com/Thread-export-not-working

The only thing that does not match with your recommendations is that I made a crop angle adjustment and animated it with LRT.
Do you think that this is causing the issue?
Thank you

Yes, you shouldn't animate the crop in LRTimelapse/Lightroom because it will create intermediary images with different sizes/aspect ratios and the encoder might fail. All explained in the link I send you 2 posts ago.

Great, thank you very much