(See the best response by Lummox JR.)
Basically ever since a few weeks ago I've been trying to log into this one game. Shinobi Story Online. And as of lately it's been starting to download the resources, and then stop randomly between 1% and 100%. And eventually close out, making it so I can't join the game.

Clearing the Cache or re-installing BYONd doesn't work, now I'm curious as to what would cause this, or how I could possibly fix it.

Best response
It sounds like the connection is simply flaky. That could be at either end--if it only happens with the one game, it's probably the server.
70 other people are connected to the server, and I have no problem connecting to any other BYOND game...
The failure of the resource download points to a transmission issue. If one end or the other is on a wireless network that's acting up right now, that could be part of it. It's also possible it's something upstream from either ISP.
This used to happen with me with a certain game, I did the following:

First, I change the path were my cache is sent to(including my hub) in the Pref.(CTRL + P while on pager to access) then going into the Advanced tab and changing the user directory.

Then, I asked the owner/host of that game to reboot, afterwards, it worked like magic. Hope this helped you