Bukkit

If you are getting an exception when the plugin loads:
Read the exception. I know it can be hard to comprehend but it'll save us both of our time if we know what the problem is.

If it says InvalidPluginException:
Check server.properties. Are any of the property values invalid?
For example, having a letter in the port value.
This is the case if you see something like this as part of the exception:

Caused by: java.lang.NumberFormatException: For input string: "25565S"

Try updating Minequery if a newer version exists.

If it says "Error initializing Minequery" or "Cannot enable - Minequery not initialized":
Make sure the port Minequery is using isn't in use by anything else that is running and that the port is not the same as the Minecraft server itself. This is very common on shared Minecraft server hosts. If you are on a shared Minecraft host, try asking them if they have an open port for Minequery.

If it says "java.lang.reflect.InvocationTargetException" and it says further down along the lines of "Caused by: java.lang.NumberFormatException: For input string: """
Check the following properties in server.properties:

server-ip
server-port
minequery-port
max-players

If they look like "name=" then either remove it's line or add a value after the equal sign. It is okay if any of these are missing.
If there is any non-numeric digit (such as a letter) in one of those properties except for server-ip, remove them.

If you are getting repeated lost connections in your console or repeated "login attempts" from a certain IP:
This is not because of Minequery. More than likely it is due to a server list checking if you are online.

If you or a server list can't connect to Minequery externally:
Check to see if the port you are using for Minequery is allowed through the firewall for incoming connections.
If you are behind a router, check to see if the port you are using for Minequery has been port forwarded.
Minequery binds to the same IP as server-ip set in server.properties. If this IP is set to localhost (127.0.0.1) or a private IP (such as 192.168.1.100), then the outside world cannot see Minequery.

If your issue was not addressed above, please look over the comments to see if it has already been answered. If not, please post a comment regarding about your problem, pasting any error messages you receive.