Problems with program_flash utility, or is it?

It seems peculiar that you were able to build the "hello" application, given that the it looks like the eCos library failed to build. Could you create a new library and capture the build output from that library? There may be an earlier error there which will help diagnose the problem.

The only thing you seem to be doing differently from me is that you are using the "vhdl" rather than "verilog" designs. This shouldn't matter, since the PTF files should be essentially identical in the two cases.