Ninite messed up my Steam

I use Ninite to keep my plugins and basic programs up to date. But today I think it may have broken something on my system. I ran Ninite and it updated three things: Paint.NET, OpenOffice and my Flash plugin. I have done this several times before on the same computer and never had any problems. However after I ran it today Steam now takes almost 10 minutes to start (sometimes, it varies every time I try). The first time took 7 minutes, I tried again just now and it took 10 minutes. This morning I opened it in less than 20 seconds!

What the heck happened? I tried a bunch of the usual fixes, I deleted clientregistry.blob and some of the .DLLs. Those redownloaded fine when I restarted the program but Steam still hangs for a bit at the "connecting to account" stage.

Any ideas?

Is it possible the version on Ninite was not up to date and Steam is furiously patching to get up to version?

But I don't update Steam through Ninite, the only programs installed were, OpenOffice and Flash. The last time I used this exe of Ninite it only installed Flash and there were no problems. Maybe I should uninstall the other two programs?