In the Rational Team Concert application management page under Advanced Properties there is a parameter called "Maximum Query Result Set Size". The default value here is 1000. There is another property called "Full Text merge Limit" this default is set to 100. Perhaps this is what you are referring to?

I know that there is a limit of 100 work items when you perform REST queries. You can override this by adding the URL argument &size=X where 'X' is the number of results you want to allow. This can defeat pagination in REST query results if that is undesired, but will make the REST query take much longer to return results.