help with syncing iphone apps with itunes

Hi There,
I just noticed that my iphone apps aren't syncing with itunes on my imac, or at least not showing up in the app list in itunes. When my phone is syncing all the apps show up in the app tab for the iphone, but they are grayed out. When I check the box to access them I get a warning saying that syncing the apps will replace all the apps on my phone. Also when I check the box all of my purchased apps disapear from the image on itunes and only the native apple preset apps remain. Not wanting to lose all of the apps on my phone I always cancel this. When my phone is not connected to the computer none of my apps show up. Everything with my phone works fine and all of my music, notes and voice memos sync just fine. I just want to make sure that all of the apps I currently have are backed up on my computer. Does anyone know why this is happening and what can be done to fix it? Does it have anything to do with the fact that I initially was syncing my phone with another computer but switched over to the imac when I bought it in February? Thanks for any help you could offer.