Particles visible through everything! :(

Without the source code of your script, it is nearly impossible to give you a conclusive answer. One scenario which intentionally renders particles above everything else is to change its object layer from default to like transparentFX, then create a new camera whose culling mask only includes transparentFX and higher rendering depth than the main camera. I suspect your script is performing something like that.

Unless you share your scene (with minimum dependencies to reproduce the issue), there is no way for others to diagnose.