A couple of things to look at...
1. How many directories exist on the data volume these VM's reside at? (If over about 1k this is a known ESXi issue) [Does not sound like your issue, but something to check]
2. If you shutdown a vapp - run consolidate on each vapp in it -- are they still slow to start?
3. Are the same VM's slow to start if you try and stop and restart it using vCenter only? (one created with vcloud, not created in vcenter)
Not sure these are your issue; but items I have seen before