I checked the changelog to make sure this issue hadn't already been fixed since TPPI2 has an old version of Botania (version 170). http://imgur.com/a/sqF4R

The sparks were placed on top of the pools (obviously) but underneath the glass. About every 20 seconds the sparks will pop up through the glass in a clockwise fashion then return to their original position. WAILA reports that they're there and I can interact with them using the Wand of the Forest.

Maybe revision 186 fixes this issue.

You still need to try to reproduce on v190.

I have 190 and can report that this does happen still.

I made a custom instance with 190 and it doesn't happen. But if it happens to Entoarox, then that's good enough for me.

I removed all the pools and their sparks except for the corner ones, the sparks still glitch up through the glass. If I place cobblestone on top of the glass, instead of the sparks glitching up through the glass they just disappear.

@UntouchedWagons It only happens to me with sparks directly below a block and adjacent to multiple other sparks.

This is a vanilla bug.