Here is the scenario:

(1) Only one source-file tab open in Eclipse.
(2) Restart the presentation compiler to ensure no error marks are present in this tab.
(3) Do a clean build, which is successful, with no errors reported.
(4) While the build is in process, red error marks appear in the tab.
(5) When the build completes (successfully, again), the red error marks remain in the tab.
(6) The fist error reported is on the package definition: "package xyz contains object and package with same name: abc one of them needs to be removed from classpath".
(7) Red error marks remain on the screen until I restart the presentation compiler.

I suppose that the presentation compiler keeps itself busy while a clean build is started, and fails when it no longer finds compiled classes. It should probably go to sleep when the clean build is started, and refresh its state in the current tab afterwards.