SharePoint Designer 2010 Deletes Web Part Connections When Creating Page - sharepoint

Question

I have a custom ASPX page hosted in a SharePoint 2010 document library with one or more web part connections from a custom web part to a SSRS ReportViewWebPart.
The code is automatically generated based on the definition of the page (done through a custom admin interface). It should look like this (and does on most environments):
<WebPartPages:SPProxyWebPartManager runat="server" ID="SPProxyWebPartManager1">
<SPWebPartConnections>
<WebPartPages:SPWebPartConnection
ConsumerID="g_d01bedc6_69b0_4c82_ac64_208be5668ec3"
ID="g_437d9428_bdb2_4d37_927c_6e1a984432f5"
ProviderConnectionPointID="ProviderValue"
ProviderID="g_AE0B5082_A085_4ba8_AD73_A7AC41E71205">
</WebPartPages:SPWebPartConnection>
</SPWebPartConnections>
</WebPartPages:SPProxyWebPartManager>
However, we are seeing a few environments where the connections are missing, like so:
<WebPartPages:SPProxyWebPartManager runat="server" ID="SPProxyWebPartManager1">
<SPWebPartConnections>
</SPWebPartConnections>
</WebPartPages:SPProxyWebPartManager>
Logging reveals that the correct code is being pushed to the document library, so something is stripping out the SPWebPartConnection nodes when the file is added to the document library. Here is the code which adds the file:
byte[ ] byteArray = Encoding.ASCII.GetBytes( page.Definition );
Hashtable properties = new Hashtable( );
properties.Add( "DashboardID", page.ID );
SPFile newFile = folder.Files.Add( String.Format( "{0}/{1}", folder, pageName ), byteArray, properties, true );
I've checked online for examples on adding files to document libraries to make sure I wasn't missing something. AllowUnsafeUpdates is set to true for the SPWeb and it is inside of a using statement, so it should be disposed of correctly.
So far the only commonality between the sites where this is broken is SP1 for SharePoint. I'm also going through and testing each hotfix in a dev environment but I'm having no luck in finding the piece that is causing the connections to be removed.
Any help would be appreciated.