Why does my one 1099-R Box 5 for Illinois Mun Retirement fund state 5. Non-taxable amount, with an amount in it, and not Employee Contributions/etc. ?

Yes, box 5 of Form 1099-R should be  "Employee contributions/ Designated Roth
contributions or insurance premiums", but sometimes government payers modify their form slightly. 

Whether the description matches exactly or not, the amount is the non-taxable portion of the amount in box 1.