I have two bug reports:

1) The app keep bothering me with pop-ups every single time I launch it. About Lightroom version choice, about enabling multi core processing and about updating the beta versions.

2) Interface becomes a mess after a clicking the frame rate drop down menu in the export screen. Everything becomes mangled and flickering.

Those settings should be saved if you close LRTimelapse normally (not force quit etc.). Then after the next launch it will read the settings and not ask again. Exception of course are new version notifications, which you should dismiss by installing the latest version of DNG Converter and LRTimelapse. There is no support for outdated versions.
Make sure that LRTimelapse has write access to the AppData folder where it stores its configuration. You might want to whitelist C:\Program Files\LRTimelapse 6 in your Virus Scanner or any "security" software.

2.) I assume you are on Windows. There are rare cases of graphics drivers / hardware combinations that show these effects. Please follow the advices in this faq: https://forum.lrtimelapse.com/thread-14323.html