Sometimes I get the message after exporting from Lightroom and when I want to render that seq. from LRT that I have to rename, when I press yes or no the dialog box dissapears and I don't know what to do, because all I have then, is a folder with all of the images, but I don't know what to do with that, so I have to reexpoert again from LR.

Do you have any idea what I am doing wrong?

Does that message tell you about a wrong sequence numbering?
This could happen, if there were some export errors from Lightroom due to corrupted images for example.
LRTimelapse then offers to fix the numbering of the files. Normally after that the render process will succeed.
You can always trigger the rendering manually from LRTimelapse after Lightroom has finished the export, just by invoking "File / Render Video" - then "select" the appropriate Intermediary sequence created by Lightroom.