I have been having a lot of trouble deploying various apps, some of them
are snapshots and some msi. I have had these packages working and then
for some reason they have stopped working.

I have just noticed this in the help files:

"If two seperate application objects give file rights to the same file,
directory, or volume and the user is unassociated with only one of them,
then the user loses all rights even though the user mights still be
associated with the other applcation object"

This could be the problem which I am having. I have unassociated my
install user from some of my packages.

Could anyone please help clarifly this situation, what happens when I
want to unasssociate my install user from just one of the packages? Do
I have to unassociate them from every package and then re-associate and
give rights again?

Can I give rights constantly to my folder where all my packages are?