Depending what your niche is, you may struggle if none of your link building contains anchor text.
You seem to be focusing purely on building links through blog comments. Personally if i was trying to get out of being sandboxed, i wouldn't do any blog comments direct to my money site as it is a very spammy even if they are done manually. Have you looked at submitting articles? Try article marketing robot for submissions to article sites and SENuke for article submissions to Web 2.0s
Don't run NHS too much i only run this software for 6 hrs and get 2000+ External backlinks but non of them are indexed, so i stopped using NHS. I see many of the feedback about NHS that if you run too much you definitely gets sandboxed.. So be beware, i am not against NHS...
Back to your question - It is just the google dance for the new site, i also recently released new site and somehow and somewhere my keyword is dancing may be page 10-7-11-20...., Don't worry, just wait for the week.
Not to be starting anything but you have not seen anything that says running NHSEO definitely gets you deindexed.
Every case that I have seen about anyone claiming deindex, penalisation or sandbox has been a fault in the way the user has been tracking his site, a very new site that hasn't even been fully indexed yet or has simply failed to provide anyway of verifying what they claim.
Just wanted to clear that up.
If you are concerned about too many links being created by NHSEO simply run it for less time or at less threads. It is likely that with this being a new site you are experiencing the very common google dance.
With NHSEO if you enter in your website as a website it will create backlinks to all of your internal pages which will look far more natural. If you are still worried about the linking looking natural then ensure that you have different anchor texts for your different pages and that the comments being used for the profile are niche relevant and appear to be a comment from a genuine user.
If you have linking pages already then you would be well advised to add these pages in as a separate profile and use the tool to backlink those links also. This will improve the benefit that these links pass on to your sites and also will take some posting time away from your money site.
You're good at keeping track on people mentioning your software.
And again, I'm not in any way criticizing NHSEO. I pretty much, with very little web development / SEO knowledge, jumped straight into using a program I didnt fully understand.
According to many, this program is as good as the user makes it.
Oh I know you are not talking bad about my tool, you were asking and you appear to have got some answers so I have no issue with that. The first few lines were meant as a response to booster so I apologise if it appeared to be aimed at you or others in this thread, it wasn't meant that way.
The bottom half was meant as advice on how you can spread the amount of links created by No Hands SEO to your other properties as well as your money site.
Sorry for any offence I will edit my original post so it is clearer what I was trying to say.