I have the same problem, I have both 25fps and 50fps and wanted to use the 50fps shots for slow motion, but render it all out at 25fps. However, when I dropped the 50fps into a 25fps sequence (which already contained 25fps footage inside it) it was normal speed (at 100%) and when I slowed it down to 50% it looked real choppy, not like slow mo.
Is cinema tools the only way to go? I don’t ever remember having to use it, generally when I dropped 50fps into a 25fps the footage would be slow to begin with (twice as long too) and I would have to speed it up 200% for it to be normal speed…