Is there any reason that it doesn't save properly? Any strings that need to be avoided or something?

sorry, Ive no idea, I gues it is just a general save problem.

And, since you mentioned one of them, here's a few common errors when importing the models, and what causes them:

Ship is invisible except for hardpoints (engines, guns, etc)
This is a problem with the .mat file which is either missing, empty or created improperly. Most common problem is the nodes in the material library do not match the material names in the model. Other problmes include textures defined with MIPS when they're using a tga file, which needs to me MIP0 (m i p zero) and texture libraries with proper names but no file imported.

Ship is visible but the textures aren't lined up properly
This is caused by using a tga texture that was not flipped vertically before importing it into the .mat file. It could also be the result of using the wrong texture file for the model, but we won't go there

Ship is visible, and correct in space but not on bases
Could be one of a few things, either the ship is very large and the camera is actually inside the ship model. Or, the HpMount hardpoint is not placed correctly, this hardpoint needs to be somewhat below the ship's lowest point, the bottom of the ship should also be facing up in Milkshape, if not than the game sees the HpMount point as being above the ship model and the model is being displayed, just not where it can be seen. And see below on LODs if that didn't fix it...

Ship is visible in space and on (some/all) bases, but not in cutscenes or while landing at/launching from planets.
The ships LOD (level of Detail) setting in shiparch.ini is missing or incorrect. Unless your model has multiple LOD meshes (if you don't know, it doesn't) your LOD values should look something like this: lod_values = 0, 1200 the format is lod_values = 0, <max visible distance>. Allthough you may be tempted to just put 0, 999999 remember that if you model will be used in MP games there may be several of them flying around and there is no need to render the ship model farther away then it can be seen, that will only hurt the game's performance.

The game crashes when ...
This is not likely the fault of the model, instead it is either the ini files you edited or some other conflict such as autosave files. Allways do the first test run(s) of the ship on a "clean" game (no other mods) ot make your life easier.

And that's just some of what I've encountered while adding two custom ships, I'm sure there are more

Game is also crashing when you use .tga files that are a) compressed, b) not using 24bit color depth

my game keeps crashing when my ship is supposed to show up on screen. I'm 99.99% positive it is not the .ini's fault. I've checked the .mat file for typos and tried doing everything and every combination there after with the .mat file. I think it's the .tga images...

they're all 256x256, 24bit color depth, 300 PPI. The only thing is, how do you know when they are compressed? I created the files in PSP8... or 7... i don't think it much matters which version, but it's the newest one. With PSP I saved them as the .tga files, now that wouldn't save them as compressed .tga files, would it? If so how do I get them uncompressed?

When you're in the file save dialog where you name the file look for the "options" button that will show up once you select the file type (TGA). Click on that and you'll be able to set the bit depth and compression for the TGA file.

Thanks, my ship is now visible and doesn't crash FL. w00t! you guys are awesome, I owe you one.