From what I could gather earlier on IRC, the untracked stratum rejects are caused by a bug in cgminer and it doesn't not affect your accepted hashrate.
Terk checked some dudes stats, and even though said person had 40-50% rejects out of ~600Kh/s, his stats page showed ~600Kh/s accepted.

Check your statistics page and see if it matches what your client is saying.