Startup.exe is just the name of the game. For example, if you were to start playing Half Life 2, you would see HL2.exe show up under your running processes. Some games support adding parameters to the "startup.exe" file so that it starts with certain conditions. You might be able to add "-DX9" to force it to use DX9 instead of DX10. If this works depends on the game, not all of them allow this.
Most modern games allow you to go into the settings and change things. Details, DX level, shadows, etc. You should be looking to change things there.
Edit: I would not uninstall DX. DX11 is backwards compatible, so there shouldn't be any issue.