So I downloaded Arena from Beth's site and set it up with DOSBox. It runs, I figured out a good number of cycles to use so it doesn't lag anymore.
Now here's the tricky part. It runs. I can open and close the program and/or DOSBox as many times as I would like to during the day and it continues to run fine.
When I go to bed and try it the next day, an error appears when trying to run Arena.
"Illegal command: A."
So far, since I have no idea what's going on, the only way I've found to fix it is to reinstall Arena. It does this every night.
I've tried restarting my computer to see if I get the same effect. I can still run Arena then.
The only other things I can think of then is that it must have to do with standby mode or the clock resetting.

Anyone have any ideas?

Tell me what commands you enter to run Arena, and how your directories are set up and mounted. Sometimes something silly like being in the wrong directory can cause that.

(dosbox folder)\games\arena

The startup commands are all in a config file so there's no chance of them being input inconsistently from one time to the next

mount c games
c:
cd arena
arena

The only thing that changes is when I am trying to run it. Same thing happened today.

You're mounting C wrong, that or you just omitted the full directory when you typed that. Either way, this is how it'd be. Let's say C:\DOSBox\games is the folder containing your games, including the ARENA folder.

mount c C:\DOSBox\games
c:
cd arena
arena

I can see if that fixes anything, but I haven't had any trouble with Doom or Daggerfall using mount c games.

I would think if it was wrong it would just not run at all. Arena runs fine, just for one day is all.

relative vs specific linking