It's happened to me before, no idea why though. It seems that if I opened SA or UFO too soon after logging in, the fps in the corner would always display 0.0 fps (even on the replay), the game would show 0.00s "actual time" for spells, and in the results/replay the slowdown would be -1.$%. It returned to normal if I closed the game and re-opened it.
It hasn't occurred to me in quite a while though. Perhaps it was only on my previous computer.
On a somewhat related note, if the game is running too fast, it still displays 0.0% slowdown. TD and DDC run at 60.6 fps for me sometimes, and the vsync patch can be used to force faster speeds.