When I first drove the Si I noticed it too. (I though WTF have I forgot how to drive a manual?). I only have the EX and it took a few days to get the hang of it. probably more pronounced with the bigger engine and more hp.
When my bro-in-law drove my Civic he had to double clutch to keep from jerking. (he has an old Austin Healey so he is used to non synchro gears)