Answer:
Something 'thrown out of whack' is disrupted, disturbed, or disoriented from it's normal state. It is a phrase, with a negative connotation, often used to describe a system/cycle that has been changed temporarily.
"My stomach is thrown out of whack from all the junk food I've been eating recently"
"My sense of time is thrown out of whack from all the traveling I've just done"
"Ever since I banged my watch it's been thrown out of whack"
In speech, the phrase is often led by the word "all":