As can be seen in this screenshot, when I used the up button to place a spruce log above another spruce log, the orientation of the newly placed log was different from the original.

that's intended, you must select the axis, for logs and pillars

although, as previous versions of the mod respected the state, I will add another option, if no axis is selected, then use same axis as the source block.

that's intended, you must select the axis, for logs and pillars

So does that mean this wand mod isn't capable of placing a roof made of stairs in one go?

It can, you need to set the stair orientation first, in the newest version I've changed it to use the same state as the first block, or if you want to use a different orientation, look in the wand menu or use alt-x for pillars/logs and R to rotate stairs.

it seems I messed something up on last beta, stair rotation isn't working.

It works fine, I just had forgotten, I've added a switch to choose to keep the block state or use rotation/axis. only accessible from the wand menu. Ah and to use alt-x to change axis of pillars/logs, remember to check the keybinding, "x" is used by default by minecraft, change it or reset it.