By default GIMP has a checkerboard pattern built up of mid-tone gray checks. You can, however, change that in the drop down menu.
The white, black and gray only options disable checks and the transparency will be shown as a solid black, white, or gray color.
Sets the size of the checks in the pattern that indicates transparency.
If you have set the check type to white, gray, or black only, then the size will have no effect what so ever.
If you are working on an 8-Bit display, the GdkRGB subsystem of GDK will automatically figure out if it needs to install its own colormap or not. Since GIMP's plug-ins are all separate processes with their own instances of GdkRGB, it may happen that GIMP and some of its Plug-Ins choose different colormaps, resulting in color flickering.
If you encounter such behaviour, you can activate "Install Colormap" in order to force GIMP and its plug-ins to use the same colormap.
If you are working on an 8-Bit display, you can display the "Marching Ants" which show the current selection by means of a rotating colormap instead of re-drawing them all the time.