According to KB942976, system DSNs are stored in HKEY_LOCAL_MACHINE\Software\ODBC\ODBC.INI. Registry redirection is enabled for this key, meaning that system DSNs for 64-bit and 32-bit applications are separated and only visible in the corresponding version of ODBCAD32. User DSNs are stored in HKEY_CURRENT_USER\Software\ODBC\ODBC.INI for which registry redirection is not enabled. Consequently, both versions of ODBCAD32 see all user DSNs.

If you had created a 32-bit system DSN and Perl couldn't use the DSN, it must be the case that the DBI module was pulling the registry key from the 64-bit registry and using the 64-bit SQL Server ODBC Driver. Can you provide the actual error you received?