Two fills and a break fill were fine in the days of two variation arrangers. Things, however, have moved on...
Yamaha have six and a break fill, Roland have seven and a break/mute (not as good as a break/fill, IMO). But the truth is, if you had a fill for each possible transition, you would need 16 (including fill-to -same, 12 if you don't have one of those). So things are far from perfect, but as anyone that has played a conversion style from a Korg on a Yammie or Roland, just having the two fills sounds VERY strange... Kind of a trip back in time.
Leeboy has nailed it, as far as tracking the trouble down... It's all about PARTIAL fills. Every arranger can do partial fills. You hit the fill button on the two or the three, you get a partial fill, or 'pick-up' as a drummer would call it. But for a pick-up to work, it has to blend reasonably smoothly with the bar that it is PART OF...
And a two fill system only blends in with HALF of the available Variations. So two of your variations, you'd better NOT ask for a pick-up. Trouble is, as the Korg owners point out, not all styles suffer equally (depending, I guess, on how much variation there is from variation to variation

). So it's a minefield, with no warning signs...
And also, I'm sorry, but the universal way of triggering fills has been, almost since arrangers came out, that the fill triggers IMMEDIATELY, for precisely the reason of giving the player the control of whether it is a full bar fill, or half bar pick-up. So offering the band-aid of setting your fills to have to be called up in advance is a very poor solution, and one that few players, used to having instant-on for fills, will be comfortable using.
It is LONG past time for Korg to step into the 21st century with this, one of the last arranger features that it's competitors completely outshine. They made considerable efforts to provide an OS that offers SA-type functionality. But, to be honest, this lack of fills is a FAR more primary shortcoming...
It is counterproductive for Korg users to keep 'defending' this flaw. It'll get fixed a LOT faster if you make noise about it and quit downplaying it's significance. And then there'll be NOTHING left for the rest to crow about!