I find that my IDE does the same thing. I'll load a project and get erroreous errors like 'Cannot resolve unit name 'cxGraphics' at line 7'. And yet everything is running perfectly.
Unfortunately I find that the IDE is getting a little flaky with each new version. Don't get me wrong - I try to do all of my projects in Delphi - even when .Net might be 'easier'. The .Net IDE, however, is way faster than my D2006 or D2009 IDEs. Some of these might be fixed in D2010 but, as is the usual #1 complaint about Delphi, is the price.
Rant off.