Help with altera FFT

If you are convinced about location of lines, fair enough.

if your fft output doesn't use all those bits then who to blame, input swing or altera design?

I guess you have taken care of sign bit(bit index 28) and checked against overflow of your used bits e.g by clipping.

Your left/rt muxing shouldn't be a problem if you have one channel correctly muxed and sampled, muxing must be correct and don't try patching up with Re/Im trick.

Rd/Wr of data is better frozen under your control so that the monitor displays same block, better only you update it manually, this way you get same lines