Hmm, that's weird. When I load that map in the dev exe (I have all DLCs) it says:
GalaxyGenerator-AddScenarioPlanetItem Error: Unsupported EntityRef found for 'PlanetBonusTrainingAcademy'.
But then the 1st player's homeworld shows up all 3 bonuses (listed by GoaFan77 above) working correctly for me. Training Academy in particular grants +6 tac and +1 SB slots as expected.
The printed/load errors are caused by lines 700-706 which have a stray entity (not a planet) with a TrainingAcademy and similarly by lines 1372-1383 which have 2 more of those, followed by lines 2049-2055 that have a similar issue, and finally lines 2722-2727 have another one. These are all academies outside a planet section, i.e. added straight to a star's section. It would help if you describe what you were trying to do with those extra academies (not the ones from the homeworlds) that you (or GF without your knowledge) added to each star. Anyway, the original file sorta works for me as I said (modulo the printed load errors). The game engine sees as errors all those planet bonuses (training academies) added directly to stars. Additionally, your file is also missing the required "templates 0" on the last line. Here's how to fix all those errors: http://pastebin.com/qBjui5pN (this is a GNU diff).