Have there been any changes to your SAN? Are there additional VMs accessing the same LUN?
The issue could be something as simple as disk performance on the SAN.
the only change is we formatted the LUN. no vms are using at the moment. Other than one lightly used box, there are no high amounts of disk activity. It was originally exported with vmkfstools -e from an esx2 box. but I dont know if some conversion is being done.
Also, if I copy from vmfs3 to vmfs3 disks the copy is normal.
Are you running ESX 3.02?
If so do you have October's patches installed?
One of them fixes a problem with really slow performance to SMB shares