Program doesn't execute the same after save() in flash

There are things (1) that are initialized/executed at upload of the code, and there are things (2) that have to be re-initialized on power up. The save() command though saves everything, but on power down certain things (2) get lost.

Configurations/settings - for example pin modes - get saved AND are then restored before onInit() and E.on("init", function(){...})``` is called.

Post your code, then we can do an analysis. Take also a look at simple explanation how to save code that espruino run on start? conversation.