They can be, but they still share log files and banlists, among other things, and reads/writes to those things aren't thread safe from what I've read of Delphi's implementation; you basically end up with a race condition when you run off the same directory and it can cause funny things to happen. It's better to create directories for each servers configs, and symlink the binary, and maps/graphics as appropriate, from one controlling directory.
None of these problems you've outlined have been issues in the past (all of them never experienced at all)... and the reason why we have this set up is so we can utilise a server booking function for people; it just wouldn't work otherwise (apparently).
Anyway I'm trying to get this sorted since I don't actually have access to the servers I'm a gameop of, and don't know much about the technical aspects of the servers.
My problem is that at the moment, the servers seem to be working, but they do not change map after the timer is completed; nor do they restart - just sit there forever until an admin that can access via a remote.txt can change the map.
Onto admining and server configurations; no one can log into admin with an rcon (which is a huge problem problem for server bookings), and a few server commands don't seem to be functioning (namely /nextmap and none of the scripts work, though I'm not sure if that is due to not being activated or whatnot). I'm also not sure if everything is being read from the config.
I've just been told the problem from a different end, so I'm not sure if they had their queries 100% correct, I just want to know what to do. Hopefully this details the problem more thoroughly... Otherwise we'll have to go back that /nextmapless 2.5.1; which I've found to be highly annoying.