(I'm assuming that c is the mount for the hard drive install, and d is the mount from the cd, if not, it might not hurt to change it that way. Some games were a bit finicky about details like that.)
If I remember correctly, I always ran the game by going to the install on the hard drive and running from there, not the cd.
I remember a lot of games would start up automatically when installing it to run for the first time, and thereafter it would need to be started up from the hard drive. I can't remember if Warcraft 2 was one of those.

(Honestly, I can remember very few games that were run from the cd, for the simple reason that the cd would have to know where the game was installed to for writing the config and savefiles, and on which drive, which would be difficult for a read-only media. Which meant that any games that ran off a cd, would most likely have the install files on c: and at a pre-set location, which would make installing it elsewhere rather difficult, if not impossible depending on the tools being used.)

I see, yeah that makes perfect sense. It was just so frustrating, but that's exactly what happened to me. It ran after I installed it, I exited out of DOSbox to change the cycle because in Warcraft 2 it scrolls extremely quickly with cycle on auto. Next thing I know I'm locked out, so yeah it appears I'll just need to set it up to run without the CD. Thanks.

Sorry, I believe I misspoke. When I said "runs off the cd", what I meant to say was "starts from the cd".
The game will still need the cd mounted in exactly the same way it was when you installed it (or cue/bin, if you're doing that) but you'll need to start the game from the hard drive install.