I'm not aware of a minimum number of CDR files limitation, so not much help there.
On the call detail record tracker log file do you see entries like the below?
2013-04-19 15:16:17,617 [9] INFO SolarWinds.FreeTools.Logging.Logger - Reading file: /cmr_StandAloneCluster_02_201304191937_98393
2013-04-19 15:16:17,620 [9] INFO SolarWinds.FreeTools.Logging.Logger - Loading file: /cmr_StandAloneCluster_02_201304191937_98393
2013-04-19 15:16:18,026 [9] INFO SolarWinds.FreeTools.Logging.Logger - Getting result table
Or is it still complaining about not being able to parse data?
I would try another ftp client. See my screen shots for filezilla above. Can't hurt.
It's the end of my day, good luck. 
Keith