Obviously the shutter speed did control the ambient as you would expect. Your confusion seems to be because the plant is also darker when you think it shouldn't be. The subject should be illuminated equally by flash in each exposure. If not, that means your flash was contributing nothing or almost nothing to the exposure to begin with. The only way to know for sure is to use a hand-held meter and read the percentage of flash contribution. With manual flash, aperture controls flash and ambient input. If you were exposing at f/5.6, the flash should also meter about f/5.6. If the flash metered at f/3.2 but you were exposing at f/10, then the flash would probably not register enough to illuminate the plant. If the scene metered at f/5.6, you could also adjust aperture up or down to change the scene, but that also affects flash contribution. If the flash meters at f/10 but you set the camera for f/11, it not only reduces the ambient light but the flash contribution. But we usually use the shutter speed to affect ambient because shutter speed doesn't affect flash.
You're also somewhat limited with shutter speed. High speed sync works only in TTL, so with manual flash you can't achieve shutter speeds of faster than the camera's sync speed without having some of the curtain appear in the shot. So as tempting as it might be to crank the shutter speed to 1/500 to darken the ambient exposure, you won't be able to with manual flash. If shutter speeds within the sync limit are not enough, you would need to control the ambient with ISO and aperture and then match the flash to the aperture and ISO. If, for example, a reading of f/10 renders the scene dark, but you meter the flash at f/10 at a given distance, the flash will properly illuminate a subject at that distance but the rest of the scene will be dark, except for flash spill.