Another strange error.
 

I am getting an error message when I run onealex's mod. This is my 10th save and I haven't gotten it before. I am assuming it applies to the SH3.exe that is patched with hsie's and steibler's patches. It says the following- Missing .bin patches. Patches not applied. - Anybody know how to fix this?

If you think it's caused by something wrong with patches being applied in H.sie's and/or Stiebler's mods, patching your sh3.exe file with them should do the trick.
Very easy and quick to do. If you need help, just ask.

Onealex comes with the exe already patched. I don't understand how the heck it lost the patches after 10 saves. It's really weird and I have never had that happen before. I wonder what caused it? In fact when I run the option selector it works fine it just gives me the stupid error when I try to run the game.

I realize that his mod comes with the .exe already patched. But if you think for some reason that somehow there is a problem with them now, it won't hurt anything to re-patch the .exe.
Worth a shot anyway. Could be a simple fix.
In terms of what caused it if that is the problem, who knows. SH3 can be that way at times. Especially a heavily modded version of it.

I tried re patching it but it would not take. I will just delete everything and start over. Thanks for the help though John.

The fact that it wouldn't take is a sign you were on the right path as to the cause of the problems.
If you have a career going, be sure to back it up before you delete the game itself.