One common issue we seem to be seeing in FCS support is that the DTS job that transfers data from the Onepoint database to the SystemCenterReporting database begins failing. While there could be many reasons for this job failing including permissions of the user for the job etc the most common reason revolves around the SystemCenterReporting database not having enough space allocated to the database. Unfortunately many people like to breeze through installers with next,next,next and this typically works. However with FCS it will cause errors in a very short while if you do not adjust your database sizes after the initial install. For reference purposes the default sizes for the FCS databases can be found at the following link http://technet.microsoft.com/en-us/library/bb418778.aspx. The key item to notice here is that the reporting db by default is 1GB. Next I would like to reference the following link http://technet.microsoft.com/en-us/library/bb418772.aspx which points out how much space various items use in the database as well as a sizing template that generalizes approximately how large your databases should be based on your client count.
As we can see from the chart even the smallest environment with SQL Enterprise will require 6GB for 6 months of data. If we extrapolate this out we will run over our default 1GB size by the end of our first month which means we will hit SQL errors with DB sizing and the DTS job that transfers data will begin failing. There are also other side effects like the 14 day history will no populate correctly/at all and you may also hit other issues with new clients not being auto approved. So please check your DB sizes for FCS and make sure you have the reporting database sized appropriately.