No, not settings for which socket supplies the trusted timing, if that's what you mean. A detection routine may pay attention to one or another though and so be thrown off if there are DIMMs of different capabilities installed. Requiring like DIMMs certainly makes their testing efforts simpler.
BIOS memory detection code varies in quality. Most of us have seen instances where memory that meets spec fails to work reliably. It isn't always the DIMM's fault. Sometimes the BIOS author or memory controller just pushes those ratings too far. Sometimes the SPD chip actually has faulty timing values. Sometimes the BIOS doesn't do the math correctly when matching SPD values with other variables it's dealing with. The fewer variables the better, but once you know what affects compatibility you can usually make anything work.
If nothing else, at least try moving the memory around between sockets and trying the new DIMM by itself. There's always the chance the new DIMM is faulty.