FTB mod pack problems

[DodgePro]

Hey guys, I have been having an issue with the new mod pack Feed The Beast. I have a server that i paid for, minecraft bare minimum but the thing is, i install the mod pack and mods and everything (ive done tekkit and such before i know how to install) but there is an issue. not a bug report, but an issue. The most important one is all the modded ores dont spawn in AND also mystcraft worlds crash the server to the point you cant sign in. NOW!!! here's the catch. If i launch it from a .bat file. EVERYTHING loads fine doesnt crash etc etc. it doesnt make sense. Any help would be greatly appreciated, and if i can get it running, anyone who is interested in playing should contact me

Thanks
- Dodge