We are having the same sort of problem. We use SCCM with SCUP to import the updates.
I found that several of our clients won't install the 11.0.03 update on top of 11.0.02.
It turns out that the the systems where the update fail may have a "slipstreamed" version of Adobe Reader 11.0.01 or 11.0.02 installed.
If the system starts out with a base Reader 11.0.0 installation, all three updates seem to install without issues.
But we still have several systems where we will have to uninstall Reader just to install 11.0.03. Why can't the updates apply to the slipstreamed versions too?