There's been a change in behaviour with FM11's Find/Change (as you've noticed). The dialog now retains focus after a search has been performed and is modal. However, the focus of the field for ctrl-F should place it in the Text area, regardless of platform, not execute the last operation. This is buggy behaviour and I just confirmed this on my platform (regardless of whether your in Doc A or B).
Please file a bug report at the FrameMaker Bugs & Wish List (https://www.adobe.com/cfusion/mmform/index.cfm?name=wishform&product=63)