Are you using jungle tree 01 and/or jungle tree 02 by chance? If you are that is the problem, if you place the start marker to close to one of those trees you will spawn under the land.
Edit: You can fix it by changing the "collisionmode = 59" in the .fpe file to anything other than 59 and it will fix it. I change it to 1 and it works fine now.
Windows 8.1 64 bit, Intel core 2 Duo CPU E8500 @3.16 GHz 3.16 GHz, 4 GB DDR2-800 PC6400 MEM, NVIDIA GeForce 9800GT 1 GB, Creative Labs Sound Blaster Audigy SE.