For mods are you referring to those you upload or actually creating a mod yourself? For mods if you send a ticket in we can give you mod upload access or help get them installed. For creating mods sadly I have no answer on that as we do not really create mods here.
If you are uploading files directly to the server you will want to change the name of the files to your Game Server ID listed on your panel. Then zip them up with that same id as the zip name. This should correct the upload process. If you are setting a seed a different way please let us know.
Are you seeing a TLS error by chance? If so in the FTP client you would want to switch to plain FTP. If that is not the case send a ticket in and we can check on the back end for any issues.
For AI mods you should find some easy scripts located here. Within the AI post you should also find a tutorial on how to add it in. DZAI is one that has been used a lot from what I remember. https://epochmod.com/forum/forum/1-arma-2/
Sorry to hear you are seeing this issue. One thing to try is switching the map in the drop down to a different mod type and then once done switch it back to the one you wish to use. This normally fixes the issue. If not please submit a ticket and we can help get this taken care of.
If need be we can re install the mod to make sure it is not bugging up. It is possible the mod is on a different version than what we currently have installed.
Deeply sorry for this issue. We are looking into this to figure out what could be going wrong as the recent update may of changed some settings with the way the game is configured on the back end. Currently we are in contact with the developers to resolve this.