after you minimize el to tray the always on top options isn't respected, and you have to deselect and reselect it to make it work
really .. i'll add it to a bug list, thanks
if you switch el in compact mode, than back in normal mode ... then you quit (i've quit from the tray menu cause i use the tray mode and the minimize on close options) and restart you will have el in compact mode again ... and then for ever and ever you will have the compact mode at startup
this one just doesn't happen to me ... but .... preferences are saved only on some events ... maybe between you switched from compact to normal mode preferneces were saved and they were not saved after that (i think they are not saved when you quit while EL is minimized). I can make it save preferences also on mode switch (compact/normal) ...