I've recently installed SCE - everything seems to be working except I don't have any data in the hardware or software inventory reports. I've verified that client can talk to the server by https://<SCEServerFQDN>:8531/simpleauthwebservice/simpleauth.asmx. The computers are all part of the correct GP. None report "Not yet contacted". All clients appear to be getting updates.
Make sure inventoryrules.cab exists under this folder, if the folder is empty, please manually download this cab file from c:\program files\update services\inventory folder on SCE server. Then try to generate inventory again.