Yes, wage garnishments or any involuntary payments could continue even after you have been making payments under the loan rehabilitation agreement but they will not be counted toward your mandatory nine payments.
Another question, if my loan is in a collection agency, what other costs could I incur? and do private collection agencies earn a commission from payments?
The private collection agencies earn a commission for any payments you make.
I'll just make a note to inquire about my federal student loan. What happens if I rehabilitate a loan that has been defaulted on?