Last night, I posted an open question about the MSI's incorrect interpretation of the OpenOffice.org RC install. Friendly Brant Gurganus offered me a link into the OpenOffice.org qa database (thanks Brant ;^).
Here's what I can offer to help
I'd need a verbose log to identify the actual problem. For information on how to generate a verbose log, please see the Frequently Asked Questions About Windows Installer topic "How can I figure out why my package fails to install?". Once one has the verbose log, try blog topics trick to quickly finding the error in a verbose MSI log and Where can I get some help parsing the Windows Installer logs?.
The upper screen shot is due to the fact that the package extractor put the MSI into a temp folder to install from, later someone deleted the files from the temp folder, and a subsequent operation required a reference to the original source. Solution is to extract the package to a cached location or to use the instructions in the SDK for Internet Download Bootstrapping and A URL-Based Windows Installer Installation Example.
The lower screen shot is due to the above error. Logs would add value here so one can figure out why an uninstall thinks it requires source. Probably want to run ICEs on the package to confirm things are kosher.
Bug 52697 (duped to 52426)
No logs but it points to Bug 49405 which is an interesting debate about build to build upgrades. A similar debate was referenced in the press recently as A Religious Debate: Upgrade in Place vs. Reinstall. Windows Installer supports either of these scenarios but the author(s) need to do more work to get this to work correctly due to product rules, component rules and version rules.
Unfortunately, it turns out I can't help entirely without logs but I hope this provides the author(s) more insights to work from. Generally complex products can not use the XCopy paradigm and the Windows Installer is built to help out. Writing to Windows Installer takes some additional work (beyond the world of XCopy) and the payoff is rich installation and integration that consumers and corporations love.
For me, the interesting thing here is that there were a few mentions that RPM provides a better model. If folks that know that model would like to enlighten me about the differences, I'd really appreciate it. ;^)