Yes, issue is exactly the same as faced by Jason below. Fastrak is working fine in it’s GUI program, PI Manager, that comes with it, but not in Matlab. In Putty, error message returned is “2 EERROR ERROR EC -99PS 0FL 0ST 0” And you are right that "It could be that the Polhemus software sets some parameters at startup that are not being setup when using putty or matlab - it may be a matter of modifying the default setup."
I am interacting with Polhemus technical support for resolution.
In fact I am aware about 3 Labs that have Fastrak for Electrode position digitization and 2 Labs are facing the same issue. Both these labs have one thing on common that they have 7-8 year old PCs. one Lab still has Windows Xp Sp3 while other has upgraded to Windows 7 from Windows Xp Sp3. Fastrak works fine in PI Manger in both but not in Matlab or Putty.
At third Lab, Fastrak is working perfectly in Matlab, Brainstorm, Putty, 3DSpaceDx 4.5.1 software of Neuroscan and PI Manager.
One point that comes to mind is that 2 Labs where Fastrak is not working properly in Matlab and Putty, and therefore other softwares, but in PI Manger it works, is that these old PCs do not have updated serial chip drivers/firmware that these softwares use and perhaps PI Manger uses low levels serial communication, and therefore is able to work. For example, may be, Matlab, Putty or new versions of softwares like Brainstorm, 3DSpaceDX use VISA instrument drivers and latest VISA.NET Shared Components, that are not available on old PCs.
If Jason, who is facing the similar issue, also has an old PC where he has installed Brainstorm, that may confirm the above hypothesis further. Then may be, by upgrading to a newer PC would solve the problem.