The vast majority of the bb you are trying to grow live in the filter. Yes some live on the surface of the substrate, however the bb are sticky and won't be pulled off by the vacuum. I'm currently cycling as well and vacuum once a week, I haven't noticed any change after vacuuming, so I don't think its effecting my cycle much. I wouldn't be real aggressive though, try to keep the surface substrate on the surface.
Have you ever seen a nitrite reading? Since you are still seeing ammonia I would think you are still in the first phase. It took me almost a month until ammonia dropped to 0 and I started seeing nitrites, I haven't had an ammonia reading since that happened. I'm not sure about the nitrate reading, maybe a false positive? The API nitrate test can be funky, you have to shake the crap out of the bottle and hit it on a hard surface, then you have to shake the crap outta the vial.
