TypeScript won't compile all referenced files unless I open them

I use requireJS and my .ts files reference each other. I did not change anything recently but TS just like that stopped to compile files unless I open them and directly look at them. Only then will it find errors for instance.  My tsconfig.json looks like this:

tsconfig.json:

{
  "compilerOptions": {
    "target" : "ES5",
    "noEmitOnError" : false,
    "removeComments": true,
    "preserveConstEnums": true,
    "sourceMap": false,
    "version":true,
    "pretty":true,
    "allowUnreachableCode":true
  }
}

Help me Obi-wan Kenobi, you are my only hope!