issues with adding new site and permalinks

So, all of a sudden whenever I try to add a new site, it doesn’t work. It appears that wp can only populate tables and not create the wp_N* tables. I know that because there’s a new entry on wp_blogs but nothing else. And since I have a pretty good mysql knowledge I created some sites directly on phpmyadmin. But ever since I did that somethings very weird started happening.

1) permalinks with trailing slash stopped working. and sometimes after a few refreshes it starts to work again
2) permalinks to existing posts often gets redirected to other subsites like: /category/old-post/ > /newsite/old-post/. but like the previous issue, after a few refreshes it all goes back to normal.

Any ideas?

thanks.