Project converting is made wrong.
1. Old project saved as "blabla_old.ipr"
2. New project saved under old name ("blabla.ipr").
Suppose you worked first time with IDEA 4.0 (project converted to new format).
Next day you accidentally start OLD IDEA 3.0 which opens converted project but can't read it. Ok, you close IDEA 3.0 and start IDEA 4.0, but after this IDEA 4.0 can't also read blabla.ipr.
I suggest you save new project NOT under old name.