The main problem most often occurs with the photon torpedo effect. Sometimes, they just don't show up, and the torpedoes are shown as white boxes. Usually, it's the red Fed/Klingon version, but I've seen the green Rom version do this, as well, though never both at the same time. Restarting the game fixes this sometimes, but only because the problem doesn't occur with any sort of pattern that I can detect.
I'm 99.5% positive this has to do with directories and where the particle effect is looking for the appropriate textures. I can even tell you the folder it's looking for, but I'm not sure where that folder is or why it works with stock Sins particles yet. Before I change anything else, I'd like to get some feedback on my other particle project to see how it's working for others.
All of the Borg weapon effects and explosions were brand new as of the last patch. If they work for everyone then I can make the same adjustments to the other weapon effects. Please let me know if any Borg particle effects aren't working for you so I can address the issue.
In the meantime, you might want to check that all of your Sins-related files are installed in the recommended location with the correct directory tree, especially leading to the mod. (Example: Local Disk C:/users/YOUR USER NAME/AppData/Local/Ironclad Games/Sins of a Solar Empire/Mods-Entrenchment v1.05/SOA2/ALL MOD FILES)
Other textures have a knack for vanishing too. I've never seen the Defiant's pulse-phasers work. Starbases also have vanishing textures, often appearing as a single object that's colored whatever my team color is. This also happens with Tactical Cubes.
I'd need to see a picture of these vanishing starbase textures to have some idea of what you're talking about, but the team color issue has been addressed in the past. All new textures have the appropriate settings to avoid this; however, please TURN OFF your MESH TEAM COLOR setting (which is below the mesh highlight filter setting) to resolve this issue with older, unmodified textures.
Finally, are you positive you're using the latest update of the mod? I'm 110% certain I fixed the texture issue with the Tactical Cube before it was released. Plus I just checked again to make sure I wasn't spreading internet lies. 
