iPhone and App Certificates and APPID''s

So I have a few questions here.

I started doing App development a while ago and am starting to submit Applications. And my question site mostly around the APPId's. Reason I am asking is because I am getting signing error's, and I think this is why.

com.Company1.App1
com.Company2.App2
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or

com.MyCompany.App1
com.MyCompany.App2

I am using the format of com.MyCompany.App1 and com.MyCompany.App2, and I have recently created the APP ID's and provisioning profiles, have them installed, have them selected in Build Settings for Distribution. I have restarted XCode done a Clean on the Apps before Building them. But it keeps giving me the error and therefore I can't upload to the App Store.

Also, I assume you just create one Certificate for all your apps, using the Company Name you have in your App Developer Profile online...correct?

UPDATE: Here is the specific error message. Also it's XCode 4 and when I goto Project->AppName->Build Settings, the correct Distribution profile is selected under Distribution.

Application failed codesign verification.  The signature was invalid, or it was not signed with an Apple submission certificate. (-19011)

Go to Target->yourapp->Get Info->Build in xcode and selected appropriate profile in code signing identity.

Let me know if you have any question.