Drag and drop worked for me, but zipalign system/sd/app didn't work. My phone (x10 mini pro) stuck at SE orb logo, but there was adb communication (i don't know if I name it right, but the program identified the phone and was able to accomplish some functions). I don't know exactly how, I removed the card in some point, a lot of reboots, but after one reboot it suddenly booted successfully, I think I pressed shell root). I had noticed that the program had stuck in "wait..." when I pressed "zipalign system/sd/app", and that launcherpro didn't work, so I pushed and installed launcherpro and magically it (LP) started working. All system apps work well, NO widget/app installed in system/sd/app works, they all crash. If I press zipalign system/sd/app again, everything is zipaligned according to the program, except launcherpro, which stops working after that and needs re-installing.
I hope I have helped you and not smothered you with this decription.
UPDATE: I started playing with root explorer, and noticed that when I added the "execute" permission to "user" some (astro, TiB) worked again, but others didn't (handcent, documents to go). Is is a matter of permissions?