I'm having a similar issue with both Collector for ArcGIS and the new Explorer for ArcGIS on Android.
If I use the 'domain/user' format, the map loads and the secure services are simply unavailable (layer is grayed out).
If I use the 'user@domain' format, the map loads and the secure services look they're trying to work, but never finish loading. When looking at the contents screen, the secure services loading icon just keeps spinning and spinning forever.
All my secure services work fine in Portal, and used to work fine in Collector as well, not sure what changed.