I have a 3 year old alu frame hybrid. Main commuter. It has been through lots of bad roads and several crashes, but checked by LBS for any cracks or faults. What I've noticed is when I pedal real hard, getting off the seat, it sort of slowes down, wiggles almost. Not sure how to define it. Maybe it was there before, but I didn't notice it. Now, compared to road bike it feels wiggly somehow when pushing it real hard. Is that what "frame flexing" feels like, is it normal?

If you have eliminated the possibility of cracks, what is your rear tire pressure like?

Quite lower than normal - yes, that could be it!