LTSpice simulation trouble
This sounds like your bias point circuit is moving or is being excited by the input waveform.  An AC analysis does an operating point analysis then uses those biases to do a small signal sweep (that's why it is so fast).  A transient analysis of course recomputes the bias as the signal changes.  The fact that running different transient analysis with different stimulations gives differing results is a big clue that your operating point is shifting as well.