Problem: Dataset with code behind repeatedly needs Run Custom Tool to compile

Maybe source code control put the vb code in the wrong place. The .vb code should be underneath the dataset in show all files, not alongside it.
Backup the current .vb code, then copy it to clipboard and delete it. Then go into the dataset and right-click > view code > then paste the code in there. The newly created .vb code file will now be behind and everything should work from now on.