What does this mean, or what is still happening when you index a project and it says it's 100% complete, but you still only have the refresh button, not an Acknowledge button (This appears some time later). Is the indexing effectively done at the initial 100% completed, or not until the Acknowledgement button appears?
In an example, a project with many issues (10k+) is indexed, and the index status page indicates 100% complete at 44 minutes, 20 seconds elapsed. But it's still cycling and the Acknowledgement button doesn't appear until 2 hrs 15 minutes.