Hello.
I've only had the Incipio battery mod for a few days and so far only ever charged it with the Motorola charger supplied with the phone. Today the battery mod and phone got really low (mod 0%, phone 15%). I powered off the phone and charged it with my old Nexus 6 charger. It charged to 100% but I could not see the mod charging. Powered the phone on, it gave the same "waiting to charge Moto Mod" message some of you have noticed. I decided to search around the net and found this thread. I tried unplugging the charger, the mod and everything like that but had no luck. Ultimately, while reading around various different posts for about 30 minutes, I checked my phone again and the mod was charging and at 14%. So I think the biggest thing is just waiting. When the mod gets to 0%, it takes up to 30 minutes to actually START charging.
I hope this helps someone else who is freaking out.
As for how I like the mod, I'm loving it. While at home and on wifi I got 50+ hours with medium use. Going back and forth to work with crappy 4G/3G on Wind mobile in downtown Toronto with very bad reception in my building I still got about 30 hours with medium to heavy use.