My friend had the same issue and she called the admissions office and explained the problem. They told her her payment was already received but something went wrong in between and that's why it didn't show up on pharmcas and UIC only updated the payment status on her Pharmcas last Friday or so. Don't worry! you won't lose your payment
Also, I guess they are a little slow in sending the confirmation emails saying the application is complete. I dropped off the supplemental on the 17th and they send me the email on the 20th. However, my friend submitted on the 21st and she just got the email this morning.