I generally try to avoid using the sample BizTalk MSI installer.
I've had alot more success using Scott Colestock's Deployment Framework for deploying BizTalk, and it solves alot of additional problems which the base MSI installer ignores as well. You can find that at http://www.traceofthought.com
You will have to learn NAnt to make that framework work, but it's worth it. (Not to mention NAnt is a good skill, and very portable to MSBuild under .NET 2.0)