SUI scoreboard should be fine- I doubt it would cause any problems.
One thing you might try is making a backup of your config.txt, then deleting it. Once you restart your server, a new config.txt should be generated. Use XGUI to configure the MOTD stuff, and then see if it works.
If not, it's very likely that something is going wrong with the code that's supposed to show the MOTD on join. It could be caused by a high server load on join. If possible, I would try removing EVERY other addon besides ULX/ULib and test it on sandbox. If it STILL isn't working, then let us know- I'd be happy to hop on your server and take a look myself.
(Also, side note: how big is your ulx_motd.txt file?)
EDIT: Oh, I just noticed- you're editing your server.cfg file? ULX stores most configurations in your server's data\ulx\config.txt file. The server.cfg cvars may get loaded too early, then get overwritten by defaults when ULX loads. which might be causing your issues. Try removing any ulx-related configuration from there (along with resetting your config.txt as described above) and see if that helps.