Welcome to the forum. Thanks for your question.
First, a comment about the "vinegar test". It's much worse than just "not the perfect test". It is useless; we never, ever do it in my STD clinic. Some HPV infected tissues don't turn white, and some tissues that turn white do not have HPV. That the spots on your penis didn't whiten is therefore slightly in favor of a cause other than HPV, but only slightly.
Next, the original wart: Was it a genital wart for sure? That is, did the dermatologist (or whoever operates the laser center) make a definitive diagnosis?
Now, the current brown spots. 1) Yes, warts can be "flat and brown", but it isn't typical; the large majority of flat brown spots, on the penis or anywhere else, are not warts. Therefore, it is probably something else. 2) Unfortunately, I cannot predict other causes. I'm not a dermatologist, and in general on this forum we avoid speculating about non-STD explanations.
Finally, I'll bet you could easily find a dermatologist who would a) make a specific effort to diagnose the lesion (maybe a biopsy would be necessary) and not just destroy it ("cut it out") and b) treat it, whether with laser or another method -- all for quite a bit less than $1,000.
I hope this has been helpful. Best wishes-- HHH, MD
The doctor in the laser center did say that the original lesion was a genital wart but did not biopsy it.
Is it possible that the same HPV stain would cause warts in different places that look completely different. Or if the current brown spots are genital warts would it be more likely that I caught two different strains of HPV.
Such as in my case: first one was as typically described ;obviously raised, whitish pink in color and cauliflower in appearance on the underside and the brown spots I described are on the top side and are not in a cluster but are scattered.
I'd like to help further, but this information doesn't change my opinion and advice. As I said above, my best guess is that the brown spots are not warts. If they are, I have no way of predicting whether they are due to the same or a different HPV type as your earlier wart. I imagine the same HPV strain could cause growths of different color and type, but I'm not aware of any research on this point.