i think this is a pretty widespread problem with iMessage. i have my iphone4 iMessage callerID set as my email account, and it receives iMessages from that same account. My iPad2 is setup using the same email address.
Out of 100 messages I receive on my phone, I probably miss 20 of them on the iPad. It also creates multiple threads for recipients when I send from the devices. Sometimes I will use my phone to send a message, and then 5 minutes later, I will use the phone again, and it will create a different thread for the recipient.
The implementation of iMessage across the iphone and ipad is pretty poor if you ask me. It should not be this difficult/confusing/impossible to get all iMessages to sync across multiple devices. and it should not be creating multiple threads on recipients' devices