Are you sure the visgroups are enabled in hammer?

If you decompile the map and you start it with hammer for the first time, is there poping a message up?

Some maps are protected. For example, you could create a map that has no entities whatsoever in it that gets downloaded to the client while the copy running on the server has all the entities required to make it run. The server is what actually maps the map run/work, the client just listens to commands being sent.

In general though, VMEX and decompiled maps in general are always broken by default. It's a "Best Guess" as to how the map was constructed and not a perfect copy. You should contact the original author and try and get the original VMF file so you have all the proper optimization and organization in place. VMEX fucks up a lot of stuff.