It should increase all movement speeds by 30%.
I'm guessing that since Fly already hits the flyspeed cap unslotted it's calculating the uncapped boost to actual flyspeed which is capped and, thus, coming up with a reduction in flyspeed.
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If that were the case, I don't think it'd show regardless of Hover or Fly...
Check what it's actually doing to your speed in the Combat Attributes.
Click on Powers at the top of your Power Tray, then at the top of the Powerlist Window, click on Combat Attributes and then open the Movement tab to see what your actual movement figures are, then use AM and see the results.
EDIT: The tool tip for AM from the icon under the Health Bar is wrong. The numbers for movement in those buff info windows are generally wrong when it comes to speed. See here.
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Is this a tooltip bug, or a gameplay bug? My tooltip tells me that Accelerate Metabolism lowers my flight speed by 2.29 MPH but increases my run speed by 4.87 MPH? This shows regardless of whether hover or flight are active.