<p>I have just installed a build server with a 64 bit windows server 2008 for continuous integration. </p>

<p>The reason I choose a 64 bit server was to have more than ~3Gb of RAM. I had hopes that this machine would provide blazing fast builds.</p>

<p>Unfortunately, the result are lacking greatly to say the least. My desktop provides faster builds than this server equipped with a Xeon quad core, 15k RPM SAS and 8 Gigs of RAM.</p>

<p>We use Visual C++ 2005 to compile our 32 bit application with Cygwin.</p>

<p>Could the WOW64 emulator be the bottleneck that is slowing down the build process?</p>

<p>Any pointers, comments would be greatly appreciated.</p>

<p>Regards,</p>

Since it sounds like you don't have properly versioned resources, have you tried changing the REINSTALLMODE property?
IIRC, in the default value of 'omus', it's the 'o' flag that's only allowing you to install if you have an older version.  You may try changing this from 'o' to 'e'.  Be warned that this will overwrite missing, older AND equally versioned files.
Manually adding in versions was the wrong way to start, but this should ensure that you don't have to manually bump up the version numbers to get them to install.