Thanks, I was trying to use the update stuff from GadgetFactory, the ols-fwloader worked well once I found the instructions (the GadgetFactory script used two programs).
That is the file for the second operation, the first, under 3.08 is named ols-loader and is what programs the FPGAROM file. This is the first one that fails with the given messages.
Thanks, here it is (I put a link to it in the blog post also).
Note, this does not affect the board working, but is one of the more mis-aligned via drills I have seen in the boards I have done. This happens to be an FTDI 4232H breakout board that came out very nice, a few tweaks if I do it again, but works very well.