Blender 2.5 Beta (2.53.0 r30581) Both on Windows and Linux
Steps to recreate.
1. Simply attach a static environment texture to any object.
2. Render scene. This correctly generates the map for first render.
3. Goto texture and select save environment map (bpy.ops.texture.envmap_save())
No matter where or what you call the file it will not save
Error returned is "//filename.png: no such file or directory
You can do this on the default blender file...so none attached.
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Isolated the issue.
On both windows and linux the save relative path is appending a "//" to front of file name and trying to save to that.
If you untick relative filenames in the save env map dialog it all saves correctly both on windows and linux