I have been recently diagnosed (early Nov 09) where my CD4 was 650 and viral load was 50. I was temporarily put on a PEP course for 2 days while waiting to confirm results. In Jan 10 I had another routine round of bloods taken where my viral load was again 50 and CD4 650. My doctors estimate from my resistance test i was infected within the last 6 months. I am concerned that i may have a different type of HIV that normal VL tests won't detect. Is this is a positive sign considering my CD4 is remaining constant or should i be concerned over having a non-clade B HIV type? What is the more likely scenario?

I am not sure how your doctor determined infection was 6 months ago using a resistance test, a test which requires a viral load level of at least 1000. Regardless your CD4 count is in the normal range and your viral load is undetectable and indicates that your immune system is doing a good job controlling the infection.