The issue is they seem very very close to each other; however, they don't seem to sound quite right...
get an audio track and record a duplicate through your hardware..
so then you have two tracks slightly out of time...
set your view to samples, turn on slip mode and zoom in as far as you can to the start of a waveform....
by drawing a selection from the start of the dry waveform to the start of the hardware waveform, you'll be able to see how many samples you are offset by..
might not look like much, but it'll sound weird unless it's perfect.
also, if you're doing this regularly,,,you could work out the length of time it takes as above,,,but instead of moving all your tracks and stuff,,you could send all dry tracks to a stereo aux which goes to master...
on that aux you use a time adjuster/delay plugin set to the exact sample delay that your hardware is adding..
obviously don't send hardware effected tracks to that aux......just leave them as output 1-2....
so effectively everything is delayed by the same amount (manual way of doing what ADC or mellomuse ATA does)
this is theoretcal,,,i haven't tried it, but i imagine if i was doing hardware effecting a lot in PTLE, this is probably how i'd manage it.