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.