Hi there @Anshu kumar,
I also have this issue... I have installed both the traditional Win32 version and the Store version bot both have the same problem. Re-enabling "Open Automatically at System Startup" does not solve the problem. What that does is re-add the startup entry to "HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run" registry key with the value
"C:\Program Files (x86)\Enpass\Enpass.exe" -minimize
It looks to me that the "-minimize" is being ignored because the window is never minimized, it starts opened with the window maximized.
Can you please look into this? It's very annoying to have this window opened every time I reboot my machine.