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This looks to be a classic case of performance issue when indexer is running . Infact a DB level performance issue looks to be the problem here . First you will need to see which DB operation is taking the maximum time so that specific ones can be fine-tuned .For that set the following tracing options :
Check Full Verbose tracing option and update the settings .
Navigate to view server output and clear the existing logs .
Check-in a new content and wait for the time you think it takes to complete indexing .
Then go to Server output and check the logs to see what db operations are taking maximum time .
Before this you should check with your DBA to see how good is DB health and also drop the indexes for the following tables and rebuild them :
Colmeta(if folders are enabled)
Hope this helps .