So, I can reproduce this issue (see https://issues.jboss.org/browse/JBIDE-8872) but I'm not sure that I caught the same bug.
Gregoire, could you check if Logger interface in your Project1 and Project2 are from the same jar?
For example if I add JBoss AS6 to classpath of Project1 but I use another copy of AS6 for Project2 then Logger imported in Project1 and Logger imported in Project2 are different IType's in Eclipse JDT model. I think we can fix this issue and resolve such injections even if the projects are not configured absolutely correctly but please check the paths of Logger's jars to make sure you got the same issue.
Your are right : sfl4j library version are not absolutely the same between the two project (1.5.11 and 1.5.10). When the dependencies were fixed, the warning disappears.