I had the issue myself. I had been infected earlier by one of the lil rakghouls, to no effect on the progression of the questline, so I dropped the quest and got it again. Heading back out, I again was infected by a lil one, again with no effect on the progression. This time, however, I did not reset it, went a lil further, and attacked a Ferocious Rakghoul (the big red beastie), which infected me yet again. This time, I received an on-screen message that I was infected and to proceed to the droid. Hopefully this might be a help to someone.