Im pretty sure the clerks at the office would have let me know if this was for a new matter dont ya think?

You would think, yes... but as you've experienced, they make mistakes, too.

Well fortunately i called the sheriffs office and the warrent had been cleared. If it is cleared on the sherrifs computer database does that mean it would be cleared by all the surrounding agencies such as Fresno PD and CHP?

Usually, yes, although there are some situations where it may not be. I regularly rely on the Sheriff's warrant line to check the status of client's warrants and haven't had any issue.