We experienced the same problem with SP3 Installed. Remember there are logs. In this case there is the SLM.ProductUsageCalculator.exe.log. I our case, we were getting a unique constraint error relating to one of the database tables. Here is the critical log entry:
Violation of UNIQUE KEY constraint 'UQ_ProductUsage'. Cannot insert duplicate key in object 'dbo.SLM_ProductUsageResult'
I noticed that a couple of application remained behind. This included one that was dynamic and that I changed to be a single in the monitored products. I thought that mght create duplicate values and so I deleted it and the other for good measure. Problem solved.
I am not saying this is everybody's problem, but the log file will give you a good start to find yours. If you have to raise an incident with support, they will probably want this file data.