Have you run the launcher to make sure your files are all working properly?
If so, open up your "eqclient.ini" file (make sure its definitely the P99 folder you play from, not EQlive, or anything else) and scroll down until you see "ShowSpellEffects=x", which is about 10% of the way down. I've got x as 1 on mine, and spells were working fine last I logged in. If it isn't 1, change it to 1...and see if that does anything.
Failing everything else, it might be a good idea to run Duxa's Installer - you can customise all kinds of things (spell gems, the UI, etc). It doesn't say it on there but I'm sure my spell effects were changed to an older 1999 look when I ran it one time
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