Having the same issue.
Was not happening with the Titanium Client.
Switched to the SoF client a few weeks ago.
deleted old Titanium Spell txt files (both US and EN )
moved the SoF client spell txt files over to server (both US and EN)
Am I correct that the Spell_New table is really not used? We only need the Spell txt files (both US and EN) listed in our server directory... in my case its E:\EQEmu
Using Rev 636 from Trunk.
Really didn't notice this until today (been busy adjusting merchants, mob pathing, making quests, etc etc... everything but actually trying to play the game) It was pointed out to me by a friend who logged in with a fresh install of the SoF client.
Tested it out by making a shaman and then a druid. Both cases, would scribe the two starter spells then if I would zone, I would lose a spell. Not always the same one.
Will go back and re download the latest Rev from trunk to see if I screwed up the compile somehow (With me I wouldn't be too surprised

)