Yes, there are some compatibility issues with the RTM build of WSS 3.0, SharePoint Server 2007 and/or Project Server 2007. Download the "Trial" installer (it is the same as normal), which for some reason was updated to have SP2 slipstreamed in already.
http://www.microsoft.com/downloads/details.aspx?displaylang=en&FamilyID=ead1b060-0394-4e26-8963-fea45602f668
Supported OS details for this release are now: Supported Operating Systems: Windows Server 2003; Windows Server 2003 R2 (32-Bit x86); Windows Server 2003 R2 x64 editions; Windows Server 2008 Datacenter; Windows Server 2008 Enterprise; Windows Server 2008 R2 Datacenter; Windows Server 2008 R2 Enterprise; Windows Server 2008 R2 Standard; Windows Server 2008 Standard
If you want to install WSS 3.0 with SP2 first, use the following link: http://www.microsoft.com/downloads/details.aspx?displaylang=en&FamilyID=ef93e453-75f1-45df-8c6f-4565e8549c2a