There was a set of recently asked questions about doing something with Internet Explorer via PowerShell. All of them contain codes to launch IE from PowerShell as an object,
There's HKCU\Software\Microsoft\Internet Explorer\Main\FrameMerging registry key that prevents merging IE "frame" processes, explained here. I haven't tried it myself, but I think it might solve your problem if you set it before you instantiate the InternetExplorer.Application COM object.
If that doesn't help, try launching a new IE instance with the following command line, prior to creating the COM object (I haven't tried that, either):
iexplore.exe -noframemerging -private -embeddingThere is a possible race condition before this IE instance becomes available as a COM server, so you may want to put some delay before you create an object.