I played on 1.4.7 and built a minecart track. Then I changed version to 13w03a because I wanted to test the new blocks and all minecarts were gone.
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I can confirm it. I am not sure in how far this bug is happening, but I only noticed it with one minecart (I had no other minecarts) which was placed in 13w01a/b. Then I changed back to 1.4.6 and the minecart was still there. And after I loaded 13w03a, it disappeared.
Can still not reproduce.
Created a world in 1.4.7 then loaded with 13w02b and 13w03a - all minecarts there.
Please force a crash by pressing F3 + C for 10 seconds while ingame and attach the crash report here.