This happens in v2.15.
If a page sends two conversion calls that are processed in the same second, only the first one is saved to the database. This prevents from recording several conversions that happen in the same page at the same time and you don't want to (or you can't) record those as several items for the same conversion.
Currently this is due to the primary key in the conversions table.
Is your problem to log more than one item conversion at a time? If so you only need to set a unique item sku for tracking?
Maybe post a small example code which fails for you.