I haven't come across this before and wondered if anyone could shed any light. I have an instance of Skanner XT playing a lead part. What I've found is that if I loop a section over and over, there will come a time when this Skanner part gets quieter and quieter. It's happening at the Reaktor level because I can see the level dropping on Reaktor's meter. 
 
I have discovered that there are two ways to fix the sound once it goes quiet. The first is to close the project and relaunch it. The second is by increasing either the "Voices" or "Unison->Max Voices" values in Reaktor's function tab. If I move either of those values up by one, the sound comes back. If I move the value back down, it stays back....until the next time it goes quiet (which it inevitably does). This is really screwing with my workflow and for the life of me I can't work out why it's happening. Any ideas? 

How long a section are you looping james? Is it a skanner preseti can load up and try out?? I'd b happy to take a look.

The loop length varies but it's between 8-16 bars. The preset is called Mono Morph, it's in the pads. I'm using it as a lead - I have tweaked it quite a bit and have it going through Omnicide. 

It sounds like the patch in question has a really long decay time, that maybe you can't actually hear. When it loops you use up the voices available after a while and you no longer hear the initial attack. All the voices are tied up playing the silent bit. When you increase the available voices it crosses that threshold and you can hear the initial attacks again. Well, it makes sense to me.

ampfixer
It sounds like the patch in question has a really long decay time, that maybe you can't actually hear. When it loops you use up the voices available after a while and you no longer hear the initial attack. All the voices are tied up playing the silent bit. When you increase the available voices it crosses that threshold and you can hear the initial attacks again. Well, it makes sense to me.

That's an interesting theory given the fact that increasing the number of voices seems to fix things. However the patch really doesn't have exceptionally long delay or release times, and I've never come across this problem before despite frequently looping synths over and over. I will check it out though, thanks. 

I used to have problems with one Reaktor preset, that anytime I played a song with it, the pitch would drop by 2 steps.  Turned out that the guy who created the patch had something tied to the mod wheel, and Sonar had a parameter in Preferences about setting all controllers to zero.  Between the two, I was always ending up with the pitch being a whole step lower, til I figured out to remove the Sonar preference about setting all controllers to zero,
 
So, the above is not what is causing your weirdness, BUT it may be somewhere to look, as some Reaktor patches seem to assign weird things to the mod wheel.
 
Good luck, 
 
Bob Bone