I had the same problem. So what I did first was I set the width of the character and set the side bearings... and it didn't work... BUT THEN I applied the autohint function and then saved everything (the box with the question mark above the glyph changes from blue or blue sided to plain) and exported the font and it worked fine. So I'm not actually sure what I did, but it worked. It was making me lose my mind too. I hope this helps :-)

Thanks! Ok so mine looks the same as the image above, except there is a question mark in a square instead of a space above the glyph in the box. Any ideas what I've done wrong?

I've been having the same issue with the space glyph in Fontforge. I've set left and right side bearings in the code 32 position. The glyph in preview is showing as an empty white box instead of a grey X so it looks like the width of the glyph has been defined? However when I export the font and set type in indesign it's still coming up as the non-defined glyph box thing? What is going wrong here? It's driving me crazy trying to fix it! (It's my first time using FF though so could easily have missed something). Thanks!