Shoshin,
I can't comment on the meds side of things. However, being awoken by bad dreams, panic and holding the breath all seems to be a major part of PTSD (I am sure you know this

).
I am pretty sure that meds do effect the REM stage of sleep. It also depends on how long on the meds, how sleep deprived you have/had been?
If you google -
'Journal of Psychiatric Research: Effects of Rem sleep awakenings'. You may find some clarity over your question there?
I will check on my online Uni resources as there are lots of up to date journals that will have covered this aspect in a medical context.
IMHO dreaming, nightmares, etc etc are a part of this process to healing. Your body may be reacting to what you were dreaming (a physical response). It could well be that by 2am you are in the REM stage, which is when dreaming occurs. However, it is also the lightest part of sleep and is a stage at which a person is more likely to awaken. So as I said it could be that you are responding to whatever the brain is outputting even though you are not totally aware.
The essence of my point is that the body will find a way to out this stuff - supressing it will fade as time goes on and your body compensates to the effects of your meds.
Hope that helps my lovely friend Shoshin.
Spirit x