I'm having a very similar issue with PDFSharp 1.31.1789.0 (GDI+ build):
My ASP.NET application is running with full trust;
On my workstation, running under IIS7.5, the correct font is embedded;
On the server, running as a console application, the correct font is embedded;
On the server, running under IIS6, the wrong font is embedded;
I've tried running the AppPool as Local System or Administrator, which makes no difference. I've tried restarting the AppPool, and even restarting IIS, but I'm still getting the wrong font embedded.
Once I get a chance, I'm going to try rebooting the server. MSDN seems to indicate that fonts installed via Remote Desktop are not available to other sessions until the server is rebooted:
http://msdn.microsoft.com/en-gb/library/dd144833.aspx