In Freetube, reload is ctrl-R on Linux and Windows, and cmd-R on Mac. I have experienced the fact that if you leave a video paused for a long time (hours) then you need to refresh. If you have history active, after refreshing the video will resume from where you left, which by the way is better then actual YouTube where it will often resume from an earlier timestamp. I have not experienced the other issues you mentioned.
With the recent major update, Freetube implemented a new player which I like much better than the old one. With the new player, all keyboard shortcuts work well, that’s great for me because my Home Theatre PC is controlled by a wireless keyboard+touchpad.