I'm not sure where this started but I've been playing Shivering Isles for about 63 hours. There is greatly reduced frame rate for flames, spell effects and what seem to be bioluminescence, glowing insects like firefly roaming around Shogorath realm. For reasons unrelated to this even, I recently reinstalled Oblivion & Shivering Isles, patched the latter to version 1.2.0416, installed OBSE & a few mods: Unarmored skill, Actor Value Uncapper & Cyrodil transportation network.
Flames are easy to see, just get close to one. For spells, those that are easy to see are target destruction and conjuration, although 3rd person mode is needed for the latter. For other spells, I thought some would not have the reduced rate effect but it seem some simply have visual representation at greatly reduced speed. For targeted destruction, the point of impact will show as usually but quite slower ; and in some cases, a few points throughout the spell trajectory (between origin and target following the path). For conjuration, the effect over the head will start right away then go on slowly, in some cases blocking the vision almost completely for a few seconds ; for example, conjuring a bow will put a yellow ball over my character right away which follow her. For the effect resembling a group of fireflies, going about Shivering Isles without fast travel will usually show it within 10 minutes, I've noticed them near the roads.
Because I reinstalled everything, I assume this undesirable effect has for origin my save files. Please let me know how I can enjoy the flickering, spawning and other such effects again.