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Do they disappear from your file list or are they shown in red when you do /pl ?
I don't know...
Maybe you can give us more information about the crash.
You said, it freezes. Does really the server crash or your client?
Make sure the syntax of your config file is correct, otherwise it get's resetted at the next start of your server by the plugin.
Do you get a green message that the config file has been saved?
When does it turn back to default, directly after saving or when you start your server?
Do you still experience the issue, yesterday we deployed which fixed some bugs in the file browser. Maybe yours was also fixed 
Tekkit doesn't support SRV records, that's why a static IP address can't be offered. It's normal for Tekkit to only have the dynamic IP address available.
Unfortunately this is not solvable.
