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do you automatically load a layer properties file?
There is a second option to load a layer properties file from a technology. There should be a second flag. Maybe this one is set in the default technology?
I need to verify this, but in case of two locations I the technology .lyp should win.
I tried to reproduce the issue you mentioned, but I was not successful so far. Here is what I did:
I also tried with groups as well, but I could not reproduce any odd behaviour. Any ideas?