I use LogCombiner v1.10.4. When I tried to combine the 2 .trees files, this error appears: "Error Parsing Input Tree: Expecting ' , ' or ' ; ' after taxon label in TRANSLATE command of TREES block". I'm not sure what it means or how to amend it.
I also think that you may have problem with the taxon names. As a rule you should avoid spaces, questionmarks, dots, commas, colons or similar symbols. remove these or replace them by underscores and then try to re-run the analyses.