@Hairball: Delete the following: Mods Folder, Coremods Folded, Config Folder, BigDig.jar, Minecraft_Server.jar
Upload the 1.3.13 Server Files to your server and enjoy your game.
@socerman: Have you checked the permissions on your files and folders? maybe some of them are read only.
Couple of Bugs I found:
1. Modular Power Suites has no Keybinding for the Glove (I cant turn off the OC like in 1.3.9)
2. The MPS glow is visible through walls
3. The MPS Glove still doesn't work on a lot of woods, no support for Sakura, Redwood and the like
4. Grafter also doesn't work on in 3. mentioned Woodtypes
5. Sprinting for more than 1 second and using the Apiarist Database, Bee/Tree Analyzers while sprinting results in Client Crash http://pastebin.com/Eim3wc5z
Overall 1.1.13 feels more stable than 1.3.9 but especiall the MPS took quite a hit with features, not sure if people like living without custom colors or a glove that can't be turned off, almost makes this thing useless when building now