This looks weird.
As far as I could see, reading preferences is done via
        LyXRC::read(FileName const & filename, bool check_format)
which return true if everything is OK.
But if using '\input "some file"', we land at src/LyXRC.cpp:464

Changing as attached, cures it for me.

        Kornel

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diff --git a/src/LyXRC.cpp b/src/LyXRC.cpp
index 27d5fcf..3a8328b 100644
--- a/src/LyXRC.cpp
+++ b/src/LyXRC.cpp
@@ -460,7 +460,7 @@ LyXRC::ReturnValues LyXRC::read(Lexer & lexrc, bool check_format)
 				FileName const tmp =
 					libFileSearch(string(),
 						      lexrc.getString());
-				if (read(tmp, check_format)) {
+				if (!read(tmp, check_format)) {
 					lexrc.printError(
 					    "Error reading included file: " + tmp.absFileName());
 				}

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