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?

-Tim
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.