When you paste a clip from Spartan using the Direct paste mode, Spartan places the clip back on the Windows clipboard, sets the windows input focus back to the program you were working in and instructs it to paste in the clip by simulating the paste keys Ctrl+V.
The vast majority of Windows programs recognize Ctrl+V as paste keys. However, a few older programs may not. Of those that don't, most recognize Shift+Ins.
If you regularly work in one of these programs, you can have Spartan use Shift+Ins instead of Ctrl+V by selecting "Secondary Paste method" in the options window.