Everthing works fine until we start to test several applications. We detect a problem with ODBC connections to MS SQLServer databases (DB2 works fine).
Domino can't "see" the DSN's and we can see a lot of connections erros, after some hours of investigation we found the problem.
The Domino server isn't the 64 version but we are using Windows 2008 64.
When you register a DSN datasource using the icon on the control panel the DSN, a system DSN is only visible for 64 bit process (see this TN from MS Knowledge base).
Following the "workaround" section of the MS TN, the applications work's well.
"To work around this problem, use the appropriate version of the ODBC Administrator tool. If you build and then run an application as a 32-bit application on a 64-bit operating system, you must create the ODBC data source by using the ODBC Administrator tool in %windir%SysWOW64odbcad32.exe. To indicate the type of DSN, you can add "_32" to the 32-bit user DSNs and "_64" to the 64-bit user DSNs "
Thank's to our friend MS SQL Server DBA.