I was recently installing vCenter 4.1 U1 on and Windows 2008 R2 Server which was utilising a remote SQL 2005 Server listening on a non standard port when the "Perf Charts service experienced an internal error" reared its head.
Trawling the web and the vmware forums pointed to the following as the solution: http://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=1021202 but no matter what I did I could not get that to work. Stats.log seemed to show that the contents of vcdb.properties were being ignored.
After much head scratching I took the following steps:
1) Deleted the Server Alias created by the SQL Native Client from the registry key: HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\MSSQLServer\Client\ConnectTo
2) Modified the dsn (odbc) connection to specify hostname,port :
3) Put vcdb.properties back to its original state ie usevcdb=true
4) Restarted the VMware VirtualCenter Management Webservices service .
All fixed. This may be of use should you use a similar configuration and experience a similar issue.