Build error 0 and build still running

[RobFlum]

Hi,
I am packaging a Wise .msi which I need to create an upgrade for. I opened the .msi with IS2013 SP1 to create an .ism. The .ism won't build error-free, though it produces a .msi. I have run validation on the created msi with ORCA, and fixed most of the validation errors, but it still won't build correctly. I have only patch and upgrade validation enabled.
Here's the tail-end of the build output:

Performing Upgrading and Patching Validation
Val0002: The RemoveFile table entry 'RemoveFile1' has an InstallMode of 1. In an upgrade scenario, if the component 'RemoveFile' does not have to reinstall, the files attributed to this table entry will not be removed. You can change the InstallMode value to 3 so that the files will at least get removed on uninstall, or make sure that this RemoveFile table entry is associated with a component that will get reinstalled.
Val0002: The RemoveFile table entry 'RemoveFile2' has an InstallMode of 1. In an upgrade scenario, if the component 'RemoveFile' does not have to reinstall, the files attributed to this table entry will not be removed. You can change the InstallMode value to 3 so that the files will at least get removed on uninstall, or make sure that this RemoveFile table entry is associated with a component that will get reinstalled.
Windows validation is disabled. To enable Windows validation: on the Tools menu, click Options and select the Validation tab.
ISDEV : fatal error 0:

A messagebox displays: No database is open. Illegal operation.
The build is still running, and I have to click the stop build icon. Apparently it is trying to do something after the msi database has been closed.
If I run a commandline build with the verbose option, I don't get any errors, but I just don't trust it.
Is there any way I can get a log of what it is doing at the end after the validation?
thanks, Rob

[RobFlum]

Output of validation run from ORCA on the built msi: Is there anything here serious enough to cause a build error?

ICE03 ERROR Invalid filename/usage of wildcards; Table: RemoveFile, Column: FileName, Key(s): RemoveFile
ICE03 ERROR Invalid filename/usage of wildcards; Table: RemoveFile, Column: FileName, Key(s): RemoveFile1
ICE03 ERROR Invalid filename/usage of wildcards; Table: RemoveFile, Column: FileName, Key(s): RemoveFile2
ICE03 ERROR Invalid filename/usage of wildcards; Table: RemoveFile, Column: FileName, Key(s): RemoveFile3

Offending rows from RemoveFile table:

RemoveFile RemoveFile imageright.desktop.interop.tlb INSTALLDIR 2
RemoveFile1 RemoveFile Atalasoft.dotImage.Lib.dll INSTALLDIR 1
RemoveFile2 RemoveFile ABCpdfCE7.dll INSTALLDIR 1
RemoveFile3 RemoveFile imageright.interfaces.ffp.dll INSTALLDIR 3

validation:

ICE03 ERROR Invalid format string; Table: Registry, Column: Value, Key(s): registry575

Registry table: (I have no idea what's wrong with this; it looks fine to me)

registry575 0 CLSID\{AF0F681B-A784-46CE-8ADB-5116CF1569EB}\InProcServer32 InprocServer32 [~]x8+-AC&,[\[]=bJAChl5?JG>'x3}v0Ez_8E%[\[]8gf*gWn[~] LotusPlugin.dll

validation:

ICE04 INFO Max Sequence in Media Table is 161
ICE18 ERROR KeyPath for Component: 'Microsoft.VisualStudio.Tools.Applications.Contract.dll' is Directory: 'GAC'. The Directory/Component pair must be listed in the CreateFolders table.
ICE18 ERROR KeyPath for Component: 'Microsoft.VisualStudio.Tools.Applications.Adapter.dll' is Directory: 'GAC'. The Directory/Component pair must be listed in the CreateFolders table.
ICE18 ERROR KeyPath for Component: 'Microsoft.Office.InfoPath.Client.Internal.Host.dll' is Directory: 'GAC'. The Directory/Component pair must be listed in the CreateFolders table.
ICE18 ERROR KeyPath for Component: 'Microsoft.Office.InfoPath.Client.Internal.Host.Interop.dll' is Directory: 'GAC'. The Directory/Component pair must be listed in the CreateFolders table.

Component table: (all 4 entries similar)

Microsoft.VisualStudio.Tools.Applications.Contract.dll {4CB7AF37-9139-4D11-84B9-999FE8ECB16D} GAC 0

validation:

ICE30 WARNING The target file 'NAFEB8~1.CON|imageright.desktop.exe.config' might be installed in '[ProgramFilesFolder]\ImageRight\Clients\' by two different conditionalized components on an LFN system: 'nativesecurity.imageright.desktop.exe.config' and 'integratedsecurity.imageright.desktop.exe.config'. If the conditions are not mutually exclusive, this will break the component reference counting system.

File table:

integratedsecurity.imageright.desktop.exe.config integratedsecurity.imageright.desktop.exe.config IN5D05~1.CON|imageright.desktop.exe.config 5315 16384 141

validation:

ICE30 WARNING The target file 'NAFEB8~1.CON|imageright.desktop.exe.config' might be installed in '[ProgramFilesFolder]\ImageRight\Clients\' by two different conditionalized components on an LFN system: 'nativesecurity.imageright.desktop.exe.config' and 'integratedsecurity.imageright.desktop.exe.config'. If the conditions are not mutually exclusive, this will break the component reference counting system.

File table:

nativesecurity.imageright.desktop.exe.config nativesecurity.imageright.desktop.exe.config NAFEB8~1.CON|imageright.desktop.exe.config 5357 16384 144

validation:
ICE32 INFO ODBCDataSource table is not in database, but is listed in the _Validation table as a foreign key of Component.KeyPath
ICE32 INFO AppId table is not in database, but is listed in the _Validation table as a foreign key of Class.AppId_
validation:

ICE64 ERROR The directory ImageRight is in the user profile but is not listed in the RemoveFile table.

Directory table:

ImageRight ProgramMenuFolder IMAGER~2|ImageRight