I had day 21 blood tests done, but started my period the following day due to shorter cycle. is this why my progesterone was only 9.9 and lh 1.1?

Unusual: You should not have a 21-22 day cycle. Meaning you should not have a period that quickly. That indicates a problem with the ovaries. I am less concerned about the Progesterone and more with the hormonal output of the ovaries. You would want to have an evaluation for thyroid disease, prolactin, and ovarian failure to make sure there is nothing drastically wrong.