Good ol' EMM386.exe! Sorry, I haven't tried any Emm386 games on dosbox so I haven't encountered this - I'm gonna try some and experiment and see how to fix this. But, for now mabye some of the solutions some other people had may fix your problem.
#1: Master of Orion
"I got master of orion to work by editing my config.sys file by changing the device=c:\windows\emm386 emm286 to
device=c:\windows\emm386 RAM "
The above is user #7 on: http://gamebird.dk/games/community2.php/?gid=443
#2: Also, someone else has a similiar problem with Privateer (since their handle says "guest" I'm not sure if it's you posting - but I'll paste the link here anyway): http://www.dosgames.com/forum/viewtopic.php?t=2183
Hope some of that may help.
By the way, using DosBox - after installing Privateer into C:\Origin\Privateer for example... then once you initiate dosbox type "mount c:" at the prompt for the program to recognize c: drive... then you can navigate to the privateer directory normally.
L8R