A user reports:

"When a MERGED map is invalid, the Omnigator Error page reports the error 
as being in the merging file. For example, the error reported here is 
actually in xsl-ss.ltm:

java.io.IOException: Lexical error at file:/C:/Users/kinley/software/
ontopia-5.0.0/apache-tomcat/webapps/omnigator/WEB-INF/topicmaps/cecom-
production-to-fo-ss.ltm:66:12: expecting ,, found ':'

(The line and character numbers accurately reflect the location of the 
problem in the merged map - it is only the file id that is in error.)"

Have verified this on the command-line with a simple pair of test files.