I'm pretty sure something with PEX is causing it, but my server has been acting really funky lately and I could use some help as I'm clueless when it comes to this stuff so here's my latest log, I just did a quick start up, then a stop. http://pastebin.com/6v0ePNBp
Yes, it is most defiantly PermissionsEx. Is PermissionsEx 1.7.9? Also have you edited your Permissions file? I say this because look on line 45 column 1. There should be something like "\t "