We encounter the same issue with XME 9.0 + latest apps on iOS 9.2
The workaround you outlined works for our iPhone 5 and an iPhone 6. On the iPhone 6 we were able to just click "re-enroll" in the menu in WorxHome. This solved the issue on this device or device class.
Our iPad reacts in a different way. This is an iPad 4th. generation (A1460). Here we tried (1.) to "re-enroll" like we did on the iPhone: failed, (2.) removed all apps incl. WorxHome and tried to re-enroll: failed, and even (3.) re-tried the 2nd attempt and additionally removed the device from the DevMgr before we launched th re-enrollment process: failed.
I don't know whether the iPads are really behaving differently or if this is a single occurrance just with our device.
Anyone able to read the debugging info you get when you connect an iOS device to a Mac and launch XCode? Any hints or ideas?