I think you may be running into both a bit of bad luck and a minor bug in the theme generator code. (Note - I'm assuming you're using something like vanilla's RemnantThemeGenerator class to add the SAD systems, but I can't say for sure because I didn't see any source files packaged with your mod...)
The bad luck comes from an unlucky sector seed that doesn't generate very many systems that can be used by the RemnantThemeGenerator. Looking at the vanilla code, it only tries to add Remnant beacons to systems with either 4+ planets or 1+ habitable planets - and only if those systems have a real primary star (no nebulas, black holes, or neutron stars allowed). Unfortunately, if someone is using mods that add their own theme generators then it's actually possible to "use" up all of the good systems before the Remnants get generated. To avoid this problem you could try reducing the total number of generated SAD systems (I think Soren made a similar change to DME's Blade Breakers a while back). It won't guarantee the Remnants will find enough systems, but it will make it much more likely...
The minor bug I mentioned is only an issue if your code is based on the vanilla RemnantThemeGenerator class. A while back, I reported an issue about it ignoring the CONSTELLATION_SKIP_PROB value (
http://fractalsoftworks.com/forum/index.php?topic=14882.msg241589#msg241589), so if your code is based on the vanilla version of that class then you might be doing something similar. If that's true, then you may want to try removing the questionable "skipProb = 0f;" line to cause your theme generator to skip the occasional system and allow the Remnants the chance to claim it instead.