Adia, as far as I'm concerned, Logic 10.6.3 does NOT have a clean bill of health, despite someone here recommending it willy nilly to everyone. I've been finding some weird new anomalies happening in Logic 10.6.3's Environment, which leads me to suspect that all is not well with that version. My investigations are ongoing and I've no way of knowing yet if the Environment problem is or isn't related to your BIP problem.
Perhaps you can work around the Bounce In Place problem by simply recording the audio into Logic, in the old-school way, although of course that then involves the chores of trimming and aligning the recorded audio file in Logic.