I am experiencing this as well. With Zoiper 3.12.1 (lib v2.8.26-IPv6) and iOS 10.2 (I have not yet tried 10.2.1), the audio levels are normal when you are on a call in the Zoiper app, but if you switch to another app the volume drops to a very low level. Switching back to the app doesn't necessarily restore the normal audio volume.
I am using a UDP SIP account with "Force background" and "WiFi keep alive" enabled.