** before you do anything to it, you may want to consider restarting from scratch (i say "you should" below, but i don't want to find and replace the tone)
those last 2 do the same, but different, thing. based on what you siad, i'd bet you have a bots binaries and a db that's not setup to use bots and maybe another conflict? either way, it's best to start over. you are correct, actually, it does overwrite all the server binaries.
start from scratch with that setup new server script after you delete it all - server and db files.
if you want bots, use the setup bots command after that script finishes. it will update db and download the latest binaries needed.
setup loginserver next.
okay, i am not 100% familiar with what gets done in that new server script... so, read it as it goes, if it downloads maps, opcodes etc, you dont' have to repeat that... i'm fairly sure it does that stuff already. i'm assuming it does db, binaries, and all the basic stuff in <database> and <assets> of the installer. bots are a 'wrinkle' for some people, so it's not part of it.
One other caveat -- once done go look in your db if db_revision (sic) is not "0000" and same with bot_db [sic] not being "0000" if you did bots. that's a sign maybe somethign went wrong in the setup... if it's populated (or you saw it mentioned updating/setting up the database -- it's echoed at the end "set db_version" to "9017" or soemthing similar) all is likely good.
running some things twice can cause problems... running somethign out of order can cause problems... or may not... so re-read anything in the wiki, including the loginserver sections or any wrinkle you used in installation... make sure to do what those wrinkles required.
some info is outdated out there... so before running any sql on your own to add something, look at it in heidisql or whatever... if it says "add merc table" go look to see if it exists already... if it's there in the correct form, it's already been run and that sql may actually damage your db.
always backup... after you get it up and running then verify you can login and do things, immediately logout, shutdown server and backup everything :p
if after you do this again you run into a hiccup, don't assume it's the installation. double check all the xml and ini files for the server. e.g. i think the config xml file is not set up for a local loginserver... you'll need another google search for that with "eqemu" attached. i think i just recently posted mine in another forum... i use a local loginserver... i mention what i did and that it coudl be wrong, lol... not an expert at this stuff.
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whichever you did last is the one you are operating on of those 2.
i'm not sure if the "latest" has bots or not, tbh. Latest is just he latest code. they let it float out there a bit, first. Then it's part of the normal server files bots/nobots after no problems arise.
i look at creation date and compare to changlelog date -- that will tell you where those binaries are at.
i don't use the installer for binaries anymore, though... just db updates. the "latest" would be similar to cloning and compiling yourself, but may still be a ~day behind?
the db updates i blieve you do need to run the normal, then bots? i could be wrong, someone please correct, if so... but as far as binaries, choose 1 of the 3 options. bots, no bots, latest all contain same set of files by name only, of course.