These bug are infamous because they stay around from one version to the next.
In the registry, if a file path is specified (i.e. C:\Program Files\My App\My Program.exe) it is encoded as [!MyProgram.exe] which specifies to use the "Full short path of the file" (aka [! = 8.3 file path). When you install the MSI, the path is then restored to the registry as C:\Progra~1\MyApp~1\MyProgr~1.exe and will make some applications fail. The proper encoding should have been [#MyProgram.exe] which would give the long path name. This bug occurs in most packages since at least WPS 3.2. UPDATE: I now suspect that this bug is caused by using SmartMonitor in conjunction with Snapshot when performing a SetupCapture.
-In Setup Editor view, Tables tab, press Ctrl-F and enter [!
-When one is found, check to see if that value in the registry of the Snapshot PC has the Long path or the Short path. If its long file path change the “[!” to “[#”. Otherwise leave it as “[!”. Don't just change it for the hell.
For more info on this, lookup the SDK for the section called Formatted
BTW: You cannot perform searches in Installation Expert view in the Registry node.
This is caused by WPS encoding a registry path like this:
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Direct3D\]
The extra back slash at the end will cause the following ICE error:
ICE03 ERROR Invalid registry path; Table: Registry, Column: Key, Key(s): registry682
If you look up the path in the Installation Expert it will look fine. If you look this up in the “Registry” table, however, the path has additional “\” at the end. This is one of the “Infamous Wise Encoding Bugs”.
In WSP 4.51, Wise has noticed the problem and attempted to fix it. But instead the fix is to create duplicate entries without the extra back slash. The bad entries cause ICE errors. To fix this YOU must delete the bad entries from the “Registry” table. UPDATE: I now suspect that this bug is caused by using SmartMonitor in conjunction with Snapshot when performing a SetupCapture.
Windows Installer Editor - Installation expert
In some packages, when you delete a file, the file disappears from Installation Expert but still shows up in the tables (Files, Components, etc). You do other things and come back to Installation Expert and find the deleted file back from the dead. To fix this you must delete them from the tables. Check the RemoveFile table too!
SetupCapture picks up files in the current user's Local File\Temp even though that folder is in the exclusion file! You have to go back and make sure that it is deleted. Sub-directories in Winnt\TEMP are also included for no reason. You must delete them from the tables. Check the RemoveFile table too!
In Windows Installer Editor, Tools menu, Change Source Paths

This is a bug with all paths that start with [path variable]. Use of path variables is the default setting in WPS. For a workaround see Procedures. The functionality behind the Change all paths to relative button cannot handle “Wise Path Variable” in the source Paths. This is a big deal since Wise Package Studio v3.x to 5.1 to use “Wise Path Variable” by default!
(Please ask Wise to fix this since my bug report was ignored.)
BTW: Even if you change the “Path Type” thing at the bottom to Relative Paths, WPS still plugs the “Wise Path Variable”! Files are always added with an Absolute Source Path.