When I was doing testing, I made sure that the Device EUI printed in the console was the same as the one I specified in the TTN console.
I have now figured out what happens:
When resetting the frame counts or doing this via changing the App Key (which is what I did to fix it), and then trying powering up board, the board connects to the gateway and therefore TTN. This is also shown through the RN2903 printing out accepted.
If I enable Frame Counter Checks and press the reset button on the board or unplug the micro USB cord, the board will continue transmitting, successfully. It just takes a little while that’s all.
If I disable Frame Counter Checks and press the reset button on the board or I power off the board by unplugging the micro USB cord, the device still connects to TTN without issue.
I do not see a noticeable difference in join time between the two.
Previously, I had the application set such that Frame Counter Checks was disabled and I had to change the App Key to get it working, but I think the major issue was just that I was not patient enough. 
I believe this issue is the same as one I have had previously, but did not have the knowledge I do now to resolve it, nor did I know what was truely happening. The only difference now is that I have now tested it on OTAA and ABP.
Here is a link to my other post: RN2903 Frame Counter Inconsistency Causing Issues with TTN Console and Accepted Packets
It’s a bit annoying that I have to wait a while as it wastes a bit of power, so I am seeing if anyone would have a reason why join times can take a couple of minutes when the gateway is only about 10 metres from the node?