Note: This discussion was moved from thecommunity to the community.
Instead of using percentage based you could limit the HA slot size using the "das.slotCpuInMHz" and "das.slotMemInMB" options. There's loads of good information on this from Duncan Epping at:
You probably have some vms with much larger reservations in the larger cluster which makes the slot size much bigger and results in there being much fewer slots. Check out pages 15-21 in the Availability Guide (http://www.vmware.com/pdf/vsphere4/r41/vsp_41_availability.pdf).