So, you are selecting Autonomous on the Driver Station, then Enabling the robot?
If you've made a lot of changes then it might be best to debug the problem by creating a new robot project and copy/paste your Auto code into Autonomous Independent.
One of the simple tests you can do is to simply make some of the status lights blink in Autonomous, like this:
Let's look at Your current Robot Main first.
Does it now look like this: