Take a look at Format, Settings, Ranges, and check that the Unicode settings are shown. If no Unicode ranges are defined MS programs might have problems.
I faced the same problem, I was working on an Arabic base font, When I Calculated Unicode Ranges FC takes proper Arabic Unicode ranges. I tried calculate Code page Character rages but FC don’t automatically takes CP1256 and without CP1256 font won’t work in IE. Font work fine with Mozilla products. Later I selected manually CP1256. Now font is working in IE also,