I spent a bit of time troubleshooting this one, but I think I've got it narrowed down to two major issues:
1) If you update to the latest iTunes version (126.96.36.199), then SyncMate will no longer see a connected iOS device. Even when the device prompts whether a system should be trusted or not, SyncMate just sits there at the screen prompting you to connect your device with the USB cable. iTunes 188.8.131.52 worked just fine.
2) If you update your device to iOS version 10.0.1 (I was on 9.3.5 before), SyncMate will not be able to see the device. Same symptoms as 1) above.
The major issue here is that if you have up-to-date iOS and iTunes, SyncMate will just not work.