How do I tell the 2 versions apart by looking only at their installations?
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If you open up the properties of the BTSNTSvc.exe file (by default located in C:\Program Files\Microsoft BizTalk Server 2006), go to the version tab and look at the Product Name. If it’s R2, it will say so there. If not, it will just say Microsoft BizTalk Server 2006.
Hope that helps!