Hmm. Did you fix the IR groups issue(couple pages back there was talk about some group related bug fixed), or is it just me who has problems with groups saving? IR-2.0.0-RC3, same result if i remove other plugins. When saving a craft with IR parts, the groups i place them in wont get saved properly into the .craft file (they get saved with the default groupName = New Group Name names). And in launch some of the groups disappear...
Here is my ksp log and save, just in case: https://www.dropbox.com/sh/av8bnl87h1ir0w8/AAAY75tnmdVIrC7FmG75j7uxa?dl=0
And some pics in case my rambling was not clear: http://imgur.com/a/aa4Rr