Using the current version of the FDK (63782), I found some strange behaviour when using makeotf for TrueTypes.
When I create the TTF in the same directory as all the source files ("makeotf -r -f font.ttf") it works fine. However when I use the -o modifier to specify a different output directory ("makeotf -r -f font.ttf -o "/Users/paul/Desktop/Mijnfontje.ttf"") then makeotf generates a TrueType without GPOS and GSUB tables. Ouch.
Anyone else has the same experience? What would be a good way to circumvent it?