We had checked all the analog voltages - VDDA (Pin-40), VREF+ (Pin-39) & VSSA (Pin-38) and ferrite beads. All these voltages were ok.
Later when we replaced the MCU in two boards, all the ADCs are working fine in these two boards.
This question deserves its own thread, but anyway.
Have you checked the voltage sequencing of Vdda/vref/etc using an oscilloscope?