This may be the time stamp issue. See this thread for details:
DOSBox changes date/time of the files

I was able work around the problem by installing Duke Nukem 3D on a Windows 98 system. This left the original time stamp intact and I was able to proceed with patching. However this requires a second computer running windows 98 which I don't everyone to have.

Sorry for resurrecting an old thread but I have the same exact problem right now. I just finished Duke Nukem 3d (v1.3D) and wanted to install Plutonium Pak add-on in order to play "The Birth" episode. Installation of the patch fails.
Is there an SVN build that would preserve timestamps? Or maybe a command or a program that I could change a timestamp in DOS? (like "touch" in UNIX world).

Some suggestions for patching with 0.74 here.

The Daum build supports changing file date/time stamps (on Windows, not sure about other platforms), but you will probably have to re-install DN3D.

voivod wrote:

Or maybe a command or a program that I could change a timestamp in DOS? (like "touch" in UNIX world).

"touch" like functionality already provided by MS-DOS since version 2+
via INT 21h function AX = 5101h
http://spike.scu.edu.au/~barry/interrupts.html#ah57

and there exist dos programs that actually utilize it, such as: (DOS) Norton Utilities's File Date

1File Date, Norton Utilities 8.0, Copyright 1994 by Symantec Corporation
2
3Change the file time and date information.
4
5FD pathname [/D[date]] [/T[time]] [/P] [/S]
6
7    /D[mm-dd-yy]  Set the date to [mm-dd-yy]
8    /T[hh:mm:ss]  Set the time to [hour:minute:second].
9    /P            Pause after each screen.
10    /S            Include Subdirectories.
11
12Running FD without /D and /T will stamp the current
13date and time on all files matching the file specified.

but i'm not aware if such function were implemented by DosBox or not.

No they aren't

I think Norton Commander allows setting custom timestamps.

And it is always possible to change the timestamp from the host OS running DOSBOX.