Too many people use COBL for it to have a major unknown problem that's not a mod interaction/conflict problem. It DOES edit a number of vanilla scripts though, so conflicts aren't unlikely.
Actually, it only edits one vanilla script, GenericLoreScript, which is completely empty and unused in the vanilla game. Most modders who deal heavily with scripts are aware of this, and so avoid using that script for anything. The chance of Cobl conflicting with anything on its own is delightfully close to nil.
Even if you got the script effect silenced, the fact that it was happening may indicate a significant script conflict that could crop up in a game-breaking way later on if not resolved.
It may, but that is not inherently the case. Many very well-made mods require script effect silencers in and of themselves, particularly combat mods and some complex companion and quest mods.
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Essentially, removing COBL (despite it being an OMOD) will make the game unable to boot. I've removed anything dependant on COBL, and ensured that nothing remains in the Data files, and yet once that mod has been installed/uninstalled, Oblivion will no longer run.
I can promise that whatever is causing this for you is not a problem in Cobl, given the thousands of users who can install and uninstall it without the issue. Use Wrye Bash to check for any remaining dependencies, at the very least. Even though your issue is fine for now, at some point you may need to uninstall Cobl again, and you'll want to know where you went wrong about it last time.