Resolved!
If altering InnoDB table, buffer needs same amount of free space as the size of the table being altered. Update didn't correctly alter DB, it did receive table full warning but it completed anyway. Strange, that I didn't see any error while updating in the web interface.
I had 200MB free, so I gave it +2GB, because "piwik_log_link_visit_action" is 1.8GB. After I manually altered the table to have this custom_float field added in 1.12, it was fine and worked correctly.
If altering InnoDB table, buffer needs same amount of free space as the size of the table being altered. Update didn't correctly alter DB, it did receive table full warning but it completed anyway. Strange, that I didn't see any error while updating in the web interface.
I had 200MB free, so I gave it +2GB, because "piwik_log_link_visit_action" is 1.8GB. After I manually altered the table to have this custom_float field added in 1.12, it was fine and worked correctly.