Messages does not display

I investigated further and realised that moving the status messages block to header top region causes the messages to display but it's a weird location to display messages. That's how am using it temporarily.

The recommended block region for status message is Highlighted.
Do you see the default status message displayed properly?

No. It doesn't display in the default highlighted region but default Drupal messages like "content has been saved" displays in highlighted region.

I have further insight on this issue.
If message block is moved to the first region (header), it displays all the time. If moved to highlited region or any other region, it displays once and other times, not noticeable (because it appears under the footer as shown in the attached photo.

Update:

Status messages display normally when internal dynamic page cache is disabled.

I have been able to find a solution to this issue.
Is it possible to move it to feature request rather than bug?

The problem doesn't occur when the page is yet to be cached but when Drupal renders a cached page, it is not able to inject the dynamic error message after the paged cache is already rendered. That's why it appears below the footer. This is the reason why disabling internal dynamic page caching eliminates the problem.

The fix:
Since I use ECA module to generate the error message, I added a cache invalidate action before the error message action as seen in the attached image.