Java files not added to source control and have grey marker

While adding a whole project and delivering to a stream, I tried to build from RTC. I got compiler errors because some files are missing in source control. Instead of the regular orange rectangle in the package explorer (eclipse client) they have a grey rectangle. Have no clue what it means (couldn't find anything in the documentation). They are not in the ignore list and repeated tries to check them in have no effect (also nothing is reported). In the right click menu only checkin is enabled.

If somebody could explain what the grey rectangle means or point me to documentation which explains it that would be greatly appreciated.

Thanks