ArcGIS creates folders with a .GDB extension while ERDAS IMAGINE creates files with a .GDB extension. Each of these is a geodatabase and they do not conflict with each other.
The .GDB folder contains the new file geodatabase implementation by ESRI. The file geodatabase is new geodatabase released with ArcGIS 9.2 as an alternative to working with personal geodatabases. It is implemented as a collection of files contained within a folder stored on the file system. Instead of the .MDB extension, used by personal geodatabase, the file geodatabase folder has a .GDB extension.
The .GDB files are proxy files that Leica Geosystems uses for their implementation of a personal geodatabase.