Output classes get erased on Make after rebuild, why?

Hello.
  I've noticed that when I do

1) full rebuild of my project, output folder gets erased (that's OK) and then, classes are compiled (progress dialog shows clearing output directories, loading classes, parsing, compiling), folder gets filled (that's OK)
2) if I do Make now however, output folder gets erased and that's all (progress dialog shows synchronizing output directory, parsing (this is quick), compiling (this is quick), synchronizing output directory)
3) if I do Make again, output folder gets filled again and I can run the program. Progress dialog shows parsing, compiling (takes time again)

What's wrong? Thanks for any tips.

Regards,
  Aleš

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I've compared the output folder after #1 and #3 - they are completely the same (up to the last byte)

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