You don't say whether this started recently or if it's been going on for a long time. That could offer a clue.
Feeling guilty is saying you feel like you're not living up to some standard like the law, your religion or the family values you were taught as a child. If you grew up in a system of different values than your life today, that could have something to do with it. For example, people who were raised in a family with a strong work ethic often feel guilty when they relax or take time off and they become workaholics. People who were raised in a family where sex and nudity were considered "dirty" are often affected by guilt when they're doing normal sexual behavior.
If, as a child, you were blamed and/or punished for things you didn't understand to be wrong, that could cause it too. It would make you feel like there is always a pending crisis looming on the horizon that you don't understand.
You sound like you have a good understanding of what is expected of you today. Try to zoom in on what was different in your past that conflicts with today. If you clearly understand what's driving the feeling, you're on your way to changing. If it starts to affect your ability to function, don't be afraid to seek counseling.