The new checkbox widgets in the reconciliation window do not seem to update consistently on my machine (OS X 10.9, Gnucash 2.5.10). The situation arises when multiple checkboxes refer to the same transaction. 

I'll use myself as an example, because that is how I noticed the bug. I use multiple sub-accounts of my checking account to do cash (or 'envelope-style' budgeting). Each subaccount denotes the amount of money I wish to spend in different categories each month. If a particular trip to, say, the drugstore, involves items from multiple categories, then several of these sub-accounts of my checking account are involved in a split transaction. And of course, each paycheque involves a deposit to every single one of these subaccounts.

My bank does not care about my personal subcategories, and so when I reconcile my bank statement, I reconcile the parent checking account in Gnucash including all of its sub-accounts. In both the 2.4 series and the 2.6 series, each line of a split transaction appears as a separate entry in the reconciliation window; e.g., my paycheque appears as about a dozen separate lines, one for each sub-account. In the 2.4 series, if I clicked a checkbox for any of these lines in a reconciliation window, every other checkbox within the same transaction would change state simultaneously, e.g., if I checked or unchecked any of the boxes corresponding to my paycheque, then all other boxes would check or uncheck themselves simultaneously.

In the 2.6 series, this no longer happens. If I check a box for a single line of a split transaction, than only the box for that specific line is checked. Under the hood, however, the behaviour is the same as before: checking a single box from my paycheque in fact marks every item in the entry for my paycheque as reconciled, it just doesn't show in the reconciliation window.

There are two ways to fix this from a UI perspective. One would be to make the checkboxes behave in the same way as the 2.4 series: all boxes from the same entry must update themselves at the same time. Alternatively, one could modify the reconciliation system so that truly one line was reconciled at a time, i.e., so that the engine reflected how the user interface looks now. As it stands, however, it really doesn't work: I have to remember to check each entry once and remember which items corresponded to split transactions and which ones didn't. 

Cf. bug 342054, which is a related but less serious problem.