Area optimization in Quartus II

Is it 100% identical, or just close? Look at LUTs/Regs, etc. It's possible it wasn't able to make much difference, although in general I usually see something. If it's identical, something is wrong. If I were to take a guess, open Design Partition Window and see what the top-level is set to. If it's post-fit strict(or Ignore changes to source files is checked, which is the option in Q10.0 I believe), then it would make sense that it ignores the synthesis changes.

Also note that Quartus looks at timing constraints. So perhaps your design has really easy constraints, and so even though you're synthesizing for Speed, it may be doing a lot of Area opts. (I don't have a full handle on how timing-driven synthesis and the synthesis options work together).