Hi,
the fact that no link is needed is not true.
For the check if the CPU is in debug mode only one bit is read from a register and if it is occasionally true the check reports "Debug mode OK" although the CPU is still running.
The CPU registers are memory mapped and the map of SL3516 differs from SL3316.
So we read something else but the debug status.
Debug mode means that the CPU is halted like hitting a breakpoint. It is required because CPU registers are used for Flash access and they would be changed if CPU is still executing code.
If we correct FlashTool I am sure that the 1-17 link will be needed!
Update 2008-05-26 by HWguru:
now an updated FlashTool version with SL3516 support is available for download
here. It should be capable of flashing SL3516 based hardware like the NAS4220 and Giganas
HWguru