Make sure your pipe event doesn't have move animation box or stop animation box checked, also I make it a parallel process. To your second question, what I do is:
@> Set Move Event: This Event
: : $>Graphic: "170-Door01',0,4,0
: : $>Wait: 4 frame(s)
: : $>Graphic: "170-Door01',0,6,0
: : $>Wait: 4 frame(s)
: : $>Graphic: "170-Door01',0,8,0
: : $>Wait: 4 frame(s)
@>Wait for Move's Completion
@>Set Move Event: Player
: : $>Through On
: : $>Move Up
: : $>Change Opacity: 0
@>Wait for Move's Completion
@>Transfer Player:[xxx: Map Name], (x, y)
@>Set Move Event: Player
: : $>Through Off
: : $>Change Opacity: 255
Hope that helps.