I don't know FontForge, but with all this, it is best if you can give version numbers (e.g., InDesign CS2, CS3; Fontforge xxx, whatever). For example, there is a known bug with CS2, namely that if there are no gsub routines (ligatures would be an example), gpos routines (for example, kerning) aren't applied.
Having said that, in InDesign, when you put the cursor between the T and y, a number appears in the kerning box (the little window with an "AV" label). If it shows a (0), you have no kerning. If it shows another number, that is the kerning value InDesign is seeing. If you do have a value, is it the same as you entered in Fontforge?