Start System Scan for Intro and Credits

Extend the time period for the server maintenance time window. https://support.plex.tv/articles/201553286-scheduled-tasks/
Verify that the analysis tasks are enabled in the global server settings.

I recommend you to enable these analysis tasks one by one, starting with the least expensive one. Then give the server a few days to actually finish each task (depends of course on the amount of media in your collection).

  1. loudness analysis for music
  2. video preview thumbnails
  3. intro detection for tv show episodes
  4. sonic analysis for music
  5. credits detection for movies and episodes

Preview Thumbnails and Credits Detection have also a switch per library, so check these as well.

If you have a lot of video in older formats, like MOV, AVI, xvid etc. then you might want to disable the hidden server preference GenerateBIFKeyframesOnly
https://support.plex.tv/articles/201105343-advanced-hidden-server-settings/
Though this will prolong the time it takes to generate the preview thumbnails, it has a higher chance to actually succeed while doing so. Older video formats are frequently bad at seeking, and the transcoder might fail at skipping to the next key frame.

Ensure that there is plenty of free space in both your general /temp folder as well as on the volume which holds the Plex data folder.
Both are going to be used heavily during the analysis.