Here is the Makefile.PL output with Perl 5.8 but the same unsatisfiing results:

C:\TEMP\DBD-DB2-1.79>perl Makefile.PL

Configuring DBD::DB2...
Remember to actually read the README and CAVEATS files!

Using DB2 in "C:/PROGRA~1/IBM/SQLLIB"
System: perl5.008008 DBI1.609  MSWin32-x86-multi-thread dl_win32.xs
Compiler: cl -MD -Zi -DNDEBUG -O1 -nologo -GF -W3 -MD -Zi -DNDEBUG -O1
+ -DWIN32 -D_CONSOLE -DNO_STRICT -DHAVE_DES_FCRYPT -DNO_HASH_SEED -DUS
+E_SITECUSTOMIZE -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -DUSE_PER
+LIO -DPERL_MSVCRT_READFIX
Includes:  -I"C:/PROGRA~1/IBM/SQLLIB/include" -I"C:\Perl\site\lib/auto
+/DBI" -I"C:\Perl\lib/auto/DBI" -I"C:\Perl\site\lib/auto/DBI"
Libraries: -L"C:/PROGRA~1/IBM/SQLLIB/lib" db2cli.lib db2api.lib -L"C:/
+Programme/Microsoft Visual Studio 8/VC/LIB" -L"C:/Programme/Microsoft
+ Visual Studio 8/VC/PlatformSDK/lib" -L"C:/Programme/Microsoft Visual
+ Studio 8/SDK/v2.0/lib" -L"R:/Online-Entwicklung/SW-Architektur/Laufw
+erk-i/C_LBSDB5/libnt"

Checking if your kit is complete...
Looks good
Checking if your kit is complete...
Looks good
Writing Makefile for DBD::DB2::Constants
Writing Makefile for DBD::DB2

C:\TEMP\DBD-DB2-1.79>
[download]

That looks fine for me, all paths are correct and the DB2 libs and incs are found.