Hi,
The System Builder generated LDFs for the BF561 offer the default configuration only (the configuration itself being documented and implemented in the LDF). You will need to use a custom LDF for the setup you describe above.
The li1171 error is caused because the LDF contains the command "RESOLVE(START_SYM, START_ADDR)", which places the "start" label from the startup code (app_startup.s) at the first instruction in L1 (0xFFA00000 and 0xFF600000 for Core A and Core B, respectively).
You need the start symbol, which comes from these objects. In VisualDSP++ 5.0 this would have come from the "basiccrt.s" source file (if you added startup code and LDF) or the crt object (e.g. crt561y.doj) explicitly included by the LDF. You may find it better to start by manually adding an LDF by copying it from the "...\Blackfin\LDF\" directory, rather than having the System Builder generate your LDF automatically (as this brings with it the expectation that startup code has been added to the project, and can be linked against for the start symbol).
Regarding the li2131 warning, you can check the Linker Log xml file, as mentioned in the warning text. This will be cause by a mismatch in the init qualifier for a section - e.g. data is marked in the source as "NO_INIT", but is being placed in an output section that explicitly calls for "ZERO_INIT", for example. The help for this topic (Help: Contents: search for "li2131") is quite comprehensive - let me know if you cannot resolve it based on the advice there.
Regards,
Craig.