You mentioned VS.NET, then VS 2005 later. I'll assume you have 2005. By default, the VBP Make VS.NET action uses MSBuild to build VS2005 projects/solutions. Building in the VS2005 IDE is actually more like building with devenv.com from the command-line, which the Make VS.NET also supports (and apparently is what works for you).
http://www.visualbuild.com/Manual/vsnetoptionstab.htm
Theoretically, building either way should always have the same result, but this may be a case where it doesn't (you'd have to ask MS why that is the case).
If you can ZIP and send or post:
1) The info from Help | About | Install Info
2) The .bld file used to build
3) The .sln file and project files (no source code files)
4) A build log file (once using devenv and once using MSBuild, with the 'Display compiler command-line' option checked in both cases)
5) Is the 'doesn't work' issue a build failure, or it treating the build as up-to-date when it isn't, or ?
we can look at it and see if it is a VBP or VS issue. Thanks.