Can anyone explain this?

[Froman]

Anyone who uses SKSE (the Skyrim Script Extender) knows that you have to open the SKSE loader manually, as Steam bypasses it. This is very annoying, of course, but there is a fix that allows you to open it directly through Steam (change TESV.exe to Skyrim.exe, change skse_loader.exe to TESV.exe, and you add a line of text to skse.ini, but I can't remember what it is). So anyway, I did this and it worked. I could open skse via Steam and all was well. For the most part.

The problem is that when I opened the game this way, the game was unbearably slow. At least half as slow as before, if not slower. I thought it was just an issue with my computer, but alas it wasn't. Once I reverted back to the normal setup, everything returned to normal.

So can anyone explain why this is happening? Yes, I know I could just add skse_loader.exe as a Non-Steam game and run it that way, but the OCD in me just can't bring myself to do that.