Ok, I found out what the issue is.
This seems like a bug but I'll let you decide. In the m3u, the channels numbers were identical so when loading the m3u files using "prefer channel numbers from m3u", Channels would stack them in the webui, (I would only see 1 channel #100, using 2 m3u's). When trying to play the channel it would never cycle.
When I imported the m3u using "ignore channel numbers from m3u" I got 2 channels in the webui(9000, 9001) and on the iOS app I had it set to stack by guide info and it started cycling the channels.