The memory usage in Linux is often very high because unused memory is used as a cache (I'm not too sure a cache for what, probably for disk access). So make sure that the red bar in the upper panel is not related to cache memory. You can configure the upper bar monitor by right clicking on it and selecting Preferences. There you can select the colors for the different types of memory, set a different color for cache and User.
In the graphical memory usage the cache memory is considered as free memory (And it is technically the case as cache can be used at any moment for new programs) so this is why you see different values.