Another thing to add:
Although the mods on my client's side seem to match that of the server's mod folder, the modpack seems to work properly on singleplayer.
So today I decided to setup a RLCraft server for my friends and I. I've already setup modded servers before, so when I loaded into the world I was surprised to see that some mods were not working properly. I looked through the server files and compared it to the original zip I downloaded, and everything seems to be in order.
To be more specific:
1) No punching trees mod does not let me break flint (and opening JEI reveals that there are no flint tools)
2) Items on the ground are picked up automatically, and don't need to be right clicked
There are probably more things than this, as I haven't tried out much myself yet.
I know for a fact that some mods are working, as I can physically see some modded structures in my world. Everything is listed in the mods tab on my client so I've been a bit puzzled as to why this is happening.