In the Font Squirrel Expert options, make sure to set the 'TrueType Hinting' option to 'Keep Existing'. Either of the other options will cause the TrueType instructions (hints) to be modified, which will in turn affect the rendering of the font.
Alternatively, if you're happy with the rendering of the font directly from GWF, you can just take that file and do the base64 encoding yourself. In OS X or Linux, use the built-in base64 command in Terminal/shell:
$ base64 myfont.ttf > fontbase64.txt
For Windows, you'll need to download a program to encode in base64 (there are several free/Open Source tools available). Copy the contents of that file, then use in your CSS as:
@font-face {
font-family: 'myfont';
src: url(data:font/truetype;charset=utf-8;base64,<<copied base64 string>>) format('truetype');
font-weight: normal;
font-style: normal;
}
(Note that you may need to make some adjustments to the various @font-face info to match your particular font data; this is just an example template)
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