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I have 2 problems with Dosbox, first, when I start the game up, the mouses flashes on screen, can only move on one corner of the screen, and if I use either button, it clicks on the desktop(which is not visible) and exits the game. second, how do I remap the keys, the control squeem is annoying, but would be fine if it weren't for the mouse bug, as the first issue means I can no longer use my mouse.
Is DOSBox in fullscreen mode? If not, try pressing Alt+Enter. You can make it start in fullscreen by opening your .conf file and setting fullscreen=true. Also, changing autolock=false to autolock=true might help.

As for remapping keys, I don't remember, but that might be done in Setup.exe. Open your Dark Forces folder in one window and the DOSBox sub-folder in another window and drag Setup.exe from the former onto dosbox.exe in the latter in order to run it.
The only time this mouse doesn't seem to be an issue is when the game isn't in fullscreen