It looks as though the Amplifire has a series effects loop. You can confirm this by setting KillDry – this should then mute the signal in PRE mode.
My guess is that the problem is caused by one of two things:
1) The unit is not actually in PRE/POST mode, even though you think it is. Can you confirm that you see a PRE or POST indication as described on p.29 of the UM ?
2) You have some kind of cabling issue, where the FX loop signal is appearing at the normal input – probably weak grounds.
If it is neither of these it is hard to know what the problem is – my guess is that it is something at your end, as this is not a known issue.
KillDry does mute the signal in PRE mode, so it must be series.
1) iPad says it is in PRE/POST mode. (Pedal – General Settings – Routing)
Also, if I go into System mode it says PRE.PST (System – Utils – Route)
2) I’m using quality cables and have tried several different types of cables to try to rule out a cable issue. The only thing plugged into Input 1 is a guitar cable which is about 8′ long with my guitar connected to the other end. Have also tried several different guitars.
After some further experimentation I’ve found that it only happens with very high gain settings on my amp.
I dropped the loop send level by 6db and compensated by raising the loop return level to +6.0 db and the problem seems to go away.
I think the default loop level on the Amplifire is too hot and causing crosstalk on Input 1.