I've noticed these skin colored and brown bumps appear on my penis and shaft.

Here is a link (it may get taken down) that has better resolution uploads: http://imgur.com/a/ZAkIf

I've tried to attach pics, but this site is insanely limited...

I am pretty sexually active. I average about 2 different partners each month. I do practice safe sex, but once in awhile I don't.

In June (almost 4 months back) I noticed the small brown bumps on my shaft and just a few flesh colored bumps (as shown in the pictures).
Because I'm pretty sexually active, I thought this might be Genital Warts or something worse. I went to the Doctor AND got STD screened/tested. The doctor said it was NOT an STD, and most likely caused by either: sexual friction, bad lubricant, shaving, or hygiene/bad nutrition -- or was some natural bumps. I had my blood drawn 3 times and was screened for literally every STD. Every single one. Nothing. I tested negative for all of them.

The bumps don't itch. They don't hurt. They are soft-ish. The one that are around the base of my shaft usually are brown, and the ones on the shaft/penis are skin colored.

In between that STD screen and now, I have had 4 sexual partners, and only 1 of them I was unsafe with.

The bumps have increased in number since the STD screen. I know 4 months ago a great Doctor told me I was okay, but they haven't gone away -- they've increased a bit. I also had the 1 unsafe encounter in that time (the bumps were present before that sexual activity). I'm still paranoid they might be Genital Warts or something else.

Is there a possibility these are an STD? Is there something that STD screens can miss?

I know I shouldn't -- I also picked one off. It was easy, didn't really hurt. Bled a little bit. No puss, no white, nothing but a little bit of blood.