Try going into the Borland program, click on Options, then Directories...
Make sure all your paths listed are correct. For instance, mine are:
Include Directories D:\BC\INCLUDE
Library Directories D:\BC\LIB
Output Directory OBJ
Source Directories [blank]
Yours might be on the C: drive
I also have D:\BC31\BIN in my path statement in my (win98) autoexec.bat file, so with this set-up, I can start up Borland from any directory just by typing BC. I just cd\ to the particular source code folder I want to edit and compile before firing BC up.
Hope this helps,