They are 3 main flavors of Avidemux.

2.4 and 2.5 shares the same core. This core allows frame accurate seeking at every stage (encoding, filters,…). That's good to create very powerful filters. The problem is that they can only handle strict constant framerate video, i.e. without “holes” and without them changing (for example 24 fps↔30 fps in hybrid NTSC DVD). That ends up with out of sync error. They handle frame ordering internally to provide the 100% frame seeking accuracy. But the reordering model of H264 is to complicated, so in that case accuracy is lost.

So, in a nutshell, 2.4 and 2.5 are frame oriented, time = frameNumber * timeBase.

2.4 is a monolithic program. Everything is compiled in, it installs basically one file : avidemux2_gtk/avidemux2_qt4. 2.5 is a plugin oriented version of 2.4. Half of the functionalities are handled through a plugin system. Of course, 2.5 being a much more recent version, it benefits from a lot of improvements, mainly done by Gruntster.

2.6 is a mostly rewritten core that deals with time. It can handle (slightly) damaged stream, varying frame rate. The frame reordering is done by the decoder, so H264 video are handled like other codecs. That also implies that a lot of the frame accuracy has been lost, and the video filter subsystem is much less powerful. 2.6 has also support for VDPAU, so that editing H264 video is slighly faster.