Here's how that connection works:
When MeditechFocus_V2.exe starts it continuously looks for any instance of Meditech C/S and when it sees one (as the foreground window) it will under the covers do Connect ..stWindows -and set up a bunch of stuff to allow it to report the text and cursor position).
Then anything can use Connect "Meditech", stStream
Anything being – the BWS UI, or a C# a program referencing BostonWorkStation70.dll, etc.) and see whatever MeditechFocus_V2 is "seeing".
MeditechFocus_V2.exe also has its own UI that shows what its seeing. (the systray black B icon).
So what we need to know is, what is MeditechFocus.exe seeing.
Your original post suggested it was seeing what you were expecting? (BWS UI) – now of course since its a different rev of Meditec, it could be connecting just fine, but your C# program is expecting different text or cursor positions.
Probably best to sort this out by calling Support!