I am running a private server with ~35 mods. I recently added Better Storage, Thaumcraft 4.1, and Thermal Expansion. These mods, nor COFH core will load on the server, but work fine in the client. I recently switched the server to use the script on this page. These are the first mods I have added since I switched to the ramdisk and a new location.
Here is ForgeModLoader-server-0.log.
This is the output from ls -l. As you can see, the file permissions, owner and group are all the same. (I switched perms to 777 to test)