The stockpile common event is not set to auto run, it operates continuously, it does take a while though for the stockpiles to increase, I'll reduce the time it takes for the stockpile to increase, every 6 minutes or so it should increase.
Curious as to where you're reading common events being set to autorun, none of them are, all are either called by another event or run on Parallel, which is continuous.
The ladders aren't to high, they were set to "below character" thus non-interact able (Unless the event is set to player touch), I've fixed this. just face the ladder and hit the action button.
Please be sure that you have completed the quests involved with the coal and crystal mines in order for them to processed into the stockpiles, otherwise they don't get mined, additionally I fixed a major problem in the production line up (not enough mining upgrades causes bottle-necks in refinement, fixed it so mana crystal will always be priority when smelting, so you can always upgrade mining later.)
Also; fixed titlescreen version number, I keep forgetting to update that :P