I just faced the same problem. I opted for another tool for developing the whole solution: I found WSPBuilder much cleaner and less intrusive. It also can be used from Command line, which is great for Build files.
I modified some Nant scripts created by Bil Simser in order to compile and deploy the project and move the code from VSeWSS to WSPBuilder. It works like a charm either on my machine or on the build machine.
You can fing WSPBuilder on http://www.Codeplex.com, and these targets need nantContrib (on www.tigris.org) to work.
here are some of the targets I'm using:
<target name="build" depends="compile">
<copy todir="${build.dir}\12\">
<fileset basedir="${sharepoint.dir}\12">
<include name="**/*"/>
</fileset>
</copy>
<copy
file="${sharepoint.dir}\solutionid.txt"
tofile="${build.dir}\solutionid.txt"
/>
<call target="buildsolutionfile" />
</target>
<target name="buildsolutionfile">
<exec program="${wspbuilder.exe}" workingdir="${build.dir}">
<arg value="-BuildDDF"/>
<arg value="${debug}"/>
<arg value="-Cleanup"/>
<arg value="false"/>
<arg value="-FolderDestination"/>
<arg value="${build.dir}"/>
<arg value="-Outputpath"/>
<arg value="${build.dir}"/>
<arg value="-TraceLevel"/>
<arg value="verbose"/>
</exec>
<copy
file="${build.dir}\${package.file}"
tofile="${solution.dir}\${package.file}"/>
</target>
<target name="addsolution">
<exec program="${stsadm.exe}" verbose="${verbose}">
<arg value="-o" />
<arg value="addsolution" />
<arg value="-filename" />
<arg value="${solution.dir}\${package.file}" />
</exec>
<call target="spwait" />
</target>
<target name="spwait" description="Waits for the timer job to complete.">
<exec program="${stsadm.exe}" verbose="${verbose}">
<arg value="-o" />
<arg value="execadmsvcjobs" />
</exec>
</target>
<target name="app.pool.reset" description="Resets Sharepoint's application pool.">
<iisapppool action="Restart" pool="${apppool}" server="${server}" />
</target>
<target name="deploysolution" depends="addsolution">
<exec program="${stsadm.exe}" workingdir="${build.dir}" verbose="${verbose}">
<arg value="-o" />
<arg value="deploysolution" />
<arg value="-name" />
<arg value="${package.file}" />
<arg value="-immediate" />
<arg value="-allowgacdeployment" />
<arg value="-allcontenturls" />
<arg value="-force" />
</exec>
<call target="spwait" />
<call target="app.pool.reset" />
</target>