When you talk about the signal dropping to '5/6 bits', that would imply that the signal is adopting one of a fairly small number of discrete levels in the Y axis.
Oddly, that is something which looks as though it may be happening, but only in one image (for which your link is broken; it'll be helpful to others if you fix it):
In every other case, all I see is the number of samples per cycle of your input signal varying as you increase the signal frequency - which, of course, is entirely expected if your sample rate remains fixed.
Try triggering off the input signal instead, so at least that is completely stable on the scope trace. Then, look and see what's happening to the DAC output, and how many discrete voltage levels it adopts.
I doubt you'll be able to discern the individual levels, unless your input signal frequency is an exact fraction of the sample rate, in which case the ADC will always measure on exactly the same points of the waveform, and so the DAC will indeed output the same set of values each time.
Try setting your waveform generator to a frequency which is relatively high compared to your sample rate - say, 12 kHz (for a 48 kHz sample rate). Then try setting it to 12.01 kHz, and watch the DAC output. You should see the individual sampled points drift slowly up and down as the relative phase of the sample clock drifts with respect to the signal you're sampling.
If they drift smoothly, your design is working. If they jump in discrete steps, you may have a problem. (Try limiting the resolution by forcing some of the LSBs low in your FPGA to see the difference).