http://bugs.winehq.org/show_bug.cgi?id=26835
--- Comment #60 from Eevee eevee.wine@veekun.com 2011-04-19 23:04:47 CDT --- It looks like Steam/Portal insist on having client.dll and server.dll encrypted and signed; after running the game once with a fresh copy of client.dll, it's replaced with a file that mentions certification and VeriSign quite a lot near the end.
Not sure why NTFS would affect this.