Lots of info missing, here.  We need more if we're gonna point you in the right direction.

First off, what modelling program did you use to make the thing?

Secondly, did you use an object placer program, and if so, which?

Okay, first, to narrow down what the problem is, try placing that exact same helipad somewhere close by on the ground and saving the flight there.  If you end up starting on the ground again, your problem is with Rwy 12 and its miriad finicky moments.  If you wind up starting CONSISTENTLY on top of the pad, your problem is with Airport.

Let us know.

Are you using FS8 or 9?  I had this problem in FS8 several times, with scenery that had elevated landing pads or runways.  I don't know if its a problem in FS9 or not.  I haven't encountered it, but I haven't been using any elevated platforms yet.

  Is your crash detection turned off when you land on the object? That could be your problem if so as fs will allow you to land on any surface even water if crash detect is turned off so when you save the flight and restart it you will wind up starting under water or under the object you landed on as fs thinks the object is a non landable object in the case of water sea planes are able to land on it by setting a flag in the air file that allows it to land on water where other craft do not have this flag and will crash. I do not know if there is a solution to your problem you may have to define it as some other object other than a raised platform i would suggest you try to find a building that allows you to use it as a starting point and find out what makes it that way.
Problaly some simple little flag or something you have overlooked. 8)