Hmm..well for starters remove BC-Phoenix and JSRS2.2 if it is a dedicated server - all you need is the .bikey file in the \Keys folder for client-side mods (note this is not related to your issue but just good server practice).
Can you post your server's RPT file to pastebin and link back here for us to look at? Are you using any kind of respawn script or BIS respawn templates?