I am working on an assembly with eight total configurations, and there are five parts on certain configurations that, some if not all mates are suppressed.
I went into the "configurations properties" like some suggested, to uncheck the "suppress new features", but none of those options were selected. This only happens in certain configurations, and it seems no matter how many times I repair the mates it still wont take.
For making new assemblies it is very helpful to make sure that "Suppress new features" is checked/unchecked per your intentions.
For existing configurations you might be well served to make a Design Table allowing it to automatically create the table's contents. This will put in any dimension or state that differs between any configurations. From there you can very easily see and control suppression states, among other things.