Since Jaxx is an HD wallet, it often pulls from multiple addresses in order to collate the funds necessary to meet the demands of the transaction, resulting in a "split" transaction. Certain services (such as exchanges and crowdsales) require the full transaction amount to originate from a single address. Attempts to send to these services from Jaxx may result in some of the transactions failing, hence the "batch transaction" issue.
In order to avoid this error, copy your wallet's current address by selecting the clipboard icon, then perform a "max" Send to that address. This will "pool" your funds into that single address, which will ensure that the transaction isn't split.
ShapeShift.io users: please note that we installed the Jaxx-ShapeShift integration in part to circumvent this issue. Please only use ShapeShift.io (the site) with Jaxx if you are trading with a coin that Jaxx does not currently support. If you have attempted a transaction with Jaxx using ShapeShift.io and part of your transaction is unaccounted for due to the batch transaction issue, please contact ShapeShift directly.