I just slightly modified the design of my sump and used PVC pipe and fitting to create better shelves in the bio-chamber. I did not use any glue and I had zero problems and that pipe is completely submerged in water. I did rinse it with warm water first and wiped it with a towel....but I didn't clean it per say or anything of the like.
If you used the correct silicone, and let it rest for 3 days plus, it isn't that.
You said you ran water through the sump for a day....so it's highly unlikely that the glass or some other part in it has contaminants in it.
That leaves nothing in the sump that could have caused the problem unless it was some part of the media you put in.
What about the drip tray or anything else you added to the sump?
Otherwise, it wasn't the sump and is altogether a different issue.