When a minecart goes through a portal to or from the nether, it won't be able to go through another one unless replaced. I explained it in this video:
http://youtu.be/6YLfFMVet1k?t=4m44s
MC-9279
Minecarts through portal bug
Resolved
Duplicate
0
Zipron Brendt
(Unassigned)
Unconfirmed
Snapshot 13w05b
Retrieved
Caused by MC-5686.