My experience is that the timestamp values control the left-to-right order of tiles in strips. You can check out the .reg files in C:\Program Files\Microsoft SDKs\Windows Media Center\v5.0\Samples\Register Application for examples of the registry formatting. After registering Application1 on my test system, I have tried changing the ordering of the following 5 timestamp values in Registry.Application.1.reg and then re-starting Media Center and it causes the tiles in the custom strip to appear in different orders:
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Media Center\Extensibility\Categories\MyCompany\MyApplication1\{e59f52ca-5440-41d3-aabf-d4e1ba53add4}]
"TimeStamp"=dword:0CC919AF
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Media Center\Extensibility\Categories\MyCompany\MyApplication1\{29b8fe49-3741-469c-8d45-abc927ffbbd8}]
"TimeStamp"=dword:0CC919B0
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Media Center\Extensibility\Categories\MyCompany\MyApplication1\{97de531e-9a8a-4faa-9f1f-bbb12fe70626}]
"TimeStamp"=dword:0CC919B1
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Media Center\Extensibility\Categories\MyCompany\MyApplication1\{f5300c25-acc0-4854-b659-f71002dba97d}]
"TimeStamp"=dword:0CC919B2
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Media Center\Extensibility\Categories\MyCompany\MyApplication1\{9ba5d566-8c2a-4bc1-b248-2f93a478b5be}]
"TimeStamp"=dword:0CC919B3
You do need to make sure to stop and restart Media Center before any registry changes will take effect (in case you hadn't tried that previously - I have gotten burned by forgetting about that in the past).
To address a couple of your other comments - I don't have a good answer about why a strip is limited to 5 tiles. I wasn't a part of that decision but I think it mostly revolved around limiting visual clutter - 5 tiles will appear in the Media Center start menu when it is run in 16x9 mode without any left/right scrolling being needed to view all of the tiles. It is also pretty rare for an application to need more than a couple of entry points, and we did not want all applications to add themselves to the start menu and clutter things visually.
You are right about the discrepancy between using RegisterMceApp for application registration and yet needing to directly edit the registry to change the order of tiles. Ideally, there would be an option to control this in the registration XML file, but unfortunately that scenario wasn't discovered until it was too late to add for Windows Vista Media Center. For now, if you require specific ordering of tiles in a custom strip, you will have to modify the registry directly. However, most cases we've seen don't require specific ordering so hopefully this will be a rare scenario.
If you do need to do this, you will have to create a separate installer for 32-bit and 64-bit because a 32-bit MSI will by default will create registry keys in the WOW64 registry hive, and the 64-bit version of Media Center does not look in the WOW64 hive for this application registration information because it is running as a native 64-bit application on a 64-bit OS.
I am working on an example for creating separate 32-bit and 64-bit installers for Media Center applications to help address this scenario. I'll post it on my blog (http://blogs.msdn.com/astebner) once I am done testing my setup authoring.
Thanks! Aaron