Ok so this is wrong
If your missing that file many things wont work. Some people who made maps had a hard time to make that file but over 90 % did . If your map is missing it you can always download a new copy of the map to your game server and your redirect. Now here is where I think you have your problem the maps on your redirect and your game server are not the same. Now IF you are running a redirect for downloads and its not an exact copy of the map on your game server you will have problems. I agree that many maps do not work with linux servers but there were not so many that it was hard to fix.
So some questions
Do you use a redirect ?
Do you copy your maps from the redirect to the game server ?
Have you checked the spelling of the maps name in the maprotation compared to the name in your usermap folder on the game server and the redirect ?
Have you asked Beers for that copy of maps that do not work on the Linux servers he almost went french trying to solve this issue
Good luck and please ask away we are always willing to try to help