Hi,
First thing I'd do is check the output of the messages(ESXi) or vmkernel(ESX) when you kick off a rescan. That should show up where slowdown is.
I'm hazarding a guess is that it could be related to the way the MS box handles multiple logons with the same to a target.
If you've set it up optimised for EQL then you'll have multiple initiator connections coming off each host, some iSCSI targets don't like this and while they still work they're not optimal.
If you can put up a detailed description of your setup and the output of you log files we might be able to help out a bit more.
Cheers
Ray