If you installed both MM:S and SM on your server, MetaMod:Source will run SourceMod.
I don't see any "only metamod" at this part.
Week ago they where Valve update what stop SM working in some mods.
SM will automatically update new gamedata files but server need to be up.
Try this, go SourceMod plugins
folder and create "New folder
Drag and drop all plugins.smx
in that "New folder
", then move that "New folder
" in plugins/disabled
So you not run any SourceMod plugins when server start, to prevent crash.
*reboot (run mm:s and sm)
Wait will SourceMod start update files (You see message in SM logs).
If not, then download Sourcemod newest snapshot
Pick gamedata-folder from zip and replace yours from server.
After reboots move your Sourcemod plugins back