Why won't iTunes transfer my purchases?

I downloaded an app from a third-party app store called Tongbu Assistant. But every time I try to sync with iTunes, it always gives me an error message saying that it couldn't transfer my purchases because they are not authorized on my computer. Which dosen't really bother me all that much because I know it's because I didn't download the apps directly from iTunes. What bothers me is the fact that after it gives me that error message, it cancels the sync every time I try to download something directly from my iTunes library to my iPod. Is there any way I can get around that issue?