Your understanding is correct.  If the H9 is in Pre/Post mode and your preset is set and saved at Pre, H9 i/o 2 should pass the signal unchanged.  A few questions to get started: 

1. Is your amp's loop serial or parallel? 

2. Does this occur with any other algorithms on H9, or is it exclusive to Phaser? 

3. Is the feedback a quick burst, or is it just constant once you engage your loop?