http://pastebin.com/Wd3di2AK link to my maps notepad file

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).

I don't know what else to say... The 3 bonuses you added directly to each of the HWs work fine for me when I load your map even without the fixes I gave. I assume you have the most recent version of Sins (1.82.5006); that's what I used to test your map. Check if you can still get the FW DLC planets (e.g. Oceanic) to show up on any random maps. If not, there might be some DLC installation/activation problem on your computer...

As for adding bonuses to a given solar system (the extra academies), I don't know if it's even possible to do that. Maybe Goafan knows of an alternative way, but the game engine clearly doesn't grok it in the way you've done, i.e. adding the planet bonuses to stars doesn't do anything.

That's extremely odd. Have you used quick start or normal start? I've used quick start when I saw the bonuses on the HWs. I didn't even try normal start. Besides that, I ran out of debugging ideas... unless you have some mods enabled. Try disabling all if that's the case.

Yeah, to note, if you have to use the "explore planet" planet upgrade to reveal the bonuses (ie, normal start) and you have not set the random spawn chance of bonuses for the map to 0, you stand a chance of the bonuses being "overridden" by what ever the map randomly spawns in.  On any map of mine that I do where I "force" add planet bonuses, I always have to set the random spawn chance to 0 else some or all will not appear.