Apologies, I'm posting late here. Issue has been resolved now with help of TAC.
Yep, it was IP confliction between two log servers. Since each log has a field named irg_log_server that is the uuid of the LS that indexed the log. When RFL get a log it verifies that a LS with the same UUID exists in the file $RTDIR/conf/logServerConfig.xml/ which in this case included only a single LS. In such case, RFL discards the logs with that orig_log_server value since it cannot find in it configuration files any LS with such UUID.
After restarting log_indexer the configuration files were rebuilt and logs are seen.
Thank you everyone for your support and suggestions.
Happy New Year to all in advacne!