If you intend on using probability, then both probability and chance would need to be changed to what you had in the old system. If you didn't change chance, then yes change probability back to what it was and you'll be good to go.
If you used the script on SVN to convert your tables over, then loot will drop at the same rate it did before. The only exception would be multiple lootdrops using the same chance but different probability would not have been converted properly. If you did convert, I'd suggest restoring from a backup and forget about the conversion process. That was an oversight on my part brought to my attention in this thread. Though, I am assuming you didn't convert, since your rates are off.
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