I have had no problems with the Tamiya flat Clear (TS-80).
Someone can correct me on this if I am wrong but, using the flat black then going over it with a gloss coat like Future negates the original flat... essentially, if you are going to apply a protective coat of future once done painting, it makes no difference if you used gloss black or flat black.
The problem with mixing the flat base with Future is that if you dont know what you are doing and get a bad ratio, you end up with an opague finish (as you experienced). For my purposes, a LIGHT coat of the flat clear achieves the same result-flattening the gloss of the future- without the risk.
Just one question- when you say you used the Future to "set the decals" you did apply the future BEFORE the decals right? Making sure you didnt decal over the flat paint.