This is pretty common I think, particularly when using fast time compression. There is a thread about it somewhere, but I think what is happening is the Orbiter graphics engine is loading a base that you are flying nearby enough to "see".
The bigger and more complicated the base (surface tiles, objects, etc) can cause a little hiccup. Those that sometimes give me problems are Polygon and ASVI.
You might try the external graphics client D3D9, or OGLA to see if it'll help (it should also give you better frame rates and visual eyes candy).
Also on the Orbiter launchpad under the Extras tab, you can select (under the visualization parameters) preload textures at session start. This will make for longer load times, but will speed up the process "in-game".