Please give examples of the exact commands used.
Due to the way I believe minecarts work regarding pausing the game I would presume the game is replaying the existing loop of the riding noise upon resumption whilst also believing the minecart has just started from a standstill and creating another loop to play over it thus amplifying the sound and making it louder.
Video footage or screenshots may help to further explain the problem.
Have you tried deleting these incorrectly generated chunks via some third-party program such as MCedit. From the results of this test you could determine whether this is a slight flaw with flatland generation or the game neglecting to read the NBT tags of the save before generating these chunks and therefore generating them as it would with a normal world. This also seams to be the same issue as MC-204.
This is a suggestion not a bug and should not be here.
I believe this is not a bug and may be intentional as this has been around for a while and many big names in Minecraft have commented on this occourance in the past.
I believe that contrary to popular belief the actual directional placement of stairs has not changed but only the rendering has so stairs can only be placed North, South, East and West. It's just that when next to other stairs they choose to render an extra 8th of a block making them appear as a corner block.
Knowing this allows for easier placement of stairs and generally allows the majority of patterns to be achievable.
This is the best Mojang can do without allowing some way of toggling behaviours by either a tool, redstone or a simple right click. It would be a very specific tool if implemented and many people may with to use stairs to hide redstone wiring due to their transparent properties but a right click is easily misclicked and can be considered an annoyance.