When you say CPU and RAM limits, do you mean like in Edit Settings of the VM from vCenter? If so, any time you deploy a new copy of the VM it will have those value reset. (Deploy is when a VM is powered on in the vApp).
It sounds like you are using an Allocation Pool or Pay-Go model, which does this enforcement based on the % guarantee of CPU/Memory and may limit based on CPU speed value.
On Top of the per VM values, there are also settings on the resource pools that would be changed at deploy time as well.
What is the purpose of removing these limits? It is somewhat against the nature of the vCloud Director product to make changes in vCenter to a VM created, deployed, and managed by vCloud Director.
