Pretty sure 5.0.6 does work with the E89. You may have been given a translated interface without the E89 headers on the main page. Try the E90 menus if you are just reading codes.
You could try downloading a fresh copy of BMW Standard Tools 2.12 and use that. I don't have a link to hand but search bimmerpost and you will find a few links.
Alternatively you can use a mobile app to read the codes. If you have an Android mobile you can use MHD Flasher to read the codes from your car for free. (You would need a £2 OTG cable to connect the USB DCAN cable to the phone).
If you have an iPhone you can use an ELM 327 v 2.1 WiFi adapter and the free version of "Carly for BMW" to scan codes.
You could try downloading a fresh copy of BMW Standard Tools 2.12 and use that. I don't have a link to hand but search bimmerpost and you will find a few links.
Alternatively you can use a mobile app to read the codes. If you have an Android mobile you can use MHD Flasher to read the codes from your car for free. (You would need a £2 OTG cable to connect the USB DCAN cable to the phone).
If you have an iPhone you can use an ELM 327 v 2.1 WiFi adapter and the free version of "Carly for BMW" to scan codes.