Help! MAJOR Object Glitches

[Raxoremys]

For a while now, I've been having this problem. I'll be sitting there happily working on a map, using all the cool new objects I just got, then I head to the Cape to test it out, and half of the objects will be missing! At first I thought it might be something to do with the my_objects folder, but it doesn't do this for every non-default object.
I then thought it might be an issue with the textures for some reason. However, today I tried making a map using only default meshes and textures, and the glitch still happened(I used a default oak tree, but with the "own collision" box ticked, and the rock from the "default" list with the oak tree texture over it).
What in the hay is going on here? Can I only use the most basic, limited objects now? Help! D:

[Anathema]

There's a possibility you might have overwritten something; the same error occurred to me when I had two different maps relying on different meshes, which incidentally depended on the same file name and overwrote each-other. I'm not entirely certain, but that's my input. :3