[JavaBrewer]

That "gritty" sound is going to persist after you install the tile. Was there anything on the wood subfloor there that might have fought the thinset? Perhaps there was a dip in the floor there and the CBU did not fully seat into the thinset? The problem with the drill/syringe fix is that you might end up with a high spot in your floor if you're not careful.

I'd hate to call it good and install tile only to develop flex later - but I can't picture that with a screw down job over mortar...