As I understand you, your problem is that you are telling Eclipse to load the same program twice, and it is doing just that, with the usual bypass/xfade/mute actions.
No way around this, unless you can get your controller not to send the same MIDI Program Change twice, or have the second preset not send the Program Change at all.
You could try having the second Program Change select a non-existent program, but I'm not sure what will happen.
