When I reconcile a bank account, there are certain transactions that get created that I don't assign a category to, so they become “unassigned” by default. I leave the transactions that way so I can go back afterwards and find them by checking “unassigned” in the left hand pane and then modify each one. (In my case, they are transactions that come in as withdrawals, but are really transfers to another account. I can't change w/d to transfer while reconciling, so that's why I come back afterwards to modify them.)
The problem is, when I click on each of the highlighted transactions and make my modifications, then change the category to the proper category and save changes, the category highlight becomes unchecked on the left pane. I then have to re-check it so I can find the rest of the unassigned items. Just a little annoying really, but it doesn't seem logical.
This only seems to happen when the category is “unassigned” (maybe because that is a special kind of category?).