It's important to look at the ms, not just the percentage. In your first screenshot you're talking about less than 1ms. Unity's OnGUI actions are not super efficient, but often good enough. Were you seeing frame rate issues?
In the last screenshot it looks like something is spamming the debug console, causing the massive slowdown. What's in your console?
EDIT: Saw your note about logging. I would still try to track down what's spamming the console. You shouldn't have to turn off logging.
EDIT: Also are you using GUI actions?