Are those two instances (the ones failing) SQL Express by any chance?
btw, generally configuring the cores as you tried is not usually a good idea. Those are fairly advanced settings that usually should be left at default unless there's a really, really good reason. If you want to balance the CPU load of the instances, the windows resource manager's a better choice
http://technet.microsoft.com/en-us/library/cc755056.aspx
Gail Shaw
Microsoft Certified Master: SQL Server, MVP, M.Sc (Comp Sci)
SQL In The Wild: Discussions on DB performance with occasional diversions into recoverability