Saving a video always shortens its total time and file size.
If the test file is opened and saved 10 times, the resulting time is 11.164s and size 12.5MB. The original time is 12.363s and size 14MB.
https://rapidshare.com/files/846234364/fpstest.ts
This bug could also cause FPS problems described in this thread http://avidemux.org/smuf/index.php/topic,11384.0.html
If the test file is encoded with HuffYUV, each save shortens the file by one frame only. Avidemux does not save the last frame or more frames if there are B or P frames.