Loss of "FrontPanel Support"

So, I am developing a large HDL wrapper for a third party ASIC, using the XEM as proxy between our PC based stuff and the ASIC.

The other day, I noticed that the API calls I was making did not seem to be getting through the first layer of my HDL. (It’s a very modular design, data gets passed from one module to the next in an interesting semi-sequential manner).

Long story short, after a lot of simulation and debugging I concluded that my code was working as intended.

I then went back to my CSharp test program, and added the:

if (false == StimulatorFPGA.IsFrontPanelEnabled())
          StatusText.Text = "FrontPanel support is not available.";
          ErrorLog += "FrontPanel support is not available." + '\n';

And it started telling me that FrontPanel was not supported - and thus none of the API calls were working.

Now, here’s the kicker:
They were working several revisions ago (loading an older bit-file resolves this). And nothing serious in the HDL has changed.

What would normally cause this?
I have re-copied the *.ngc files.
Verified all of sources are up to date, DLL’s, etc.
Re-synthed/placed/routed the design several times.

…still nothing.

Just as a note, the design is at ~59/66% (FF/LUT) usage of all FPGA resources. The synthesis tool says the design should be able to work at 88MHz or so (well above the 48MHz required by the HostInterface).
Any thoughts?

PS> Is it just me, or is anyone else getting an error trying to extract the latest ModelSim simulation libraries - Windows keeps telling me the .ZIP is currupt.