Vista's version of Paint automatically saves files as jPEG by default - it's supposed to work that way.  I'm not sure why this just appeared after a Windows Update as according to what I've read, this is the default for the program itself -  see the next paragraph and link (though I suppose it's possible it carried over the old default from XP if you upgraded and didn't change until the update "corrected" it). 

In Windows Vista, the toolbar icons and default colour palette have been changed. Also, an increased number of undo levels to 10 times, a zoom slider, and a crop function have been added. This version saves as .jpg by default, which can dramatically impact the overall quality of an image, especially after multiple saves of the file due to its method of compression. http://en.wikipedia.org/wiki/Paint_(software).

I'm not sure why this JPEG differs from other JPEG files for your other programs, but I can't find a way to change the default (though I suspect there's a registry hack for this, I can't find it by searching Bing, Google, and Yahoo and the Microsoft Knowledge Base - and running through regedit with Paint as the search criterium).  I'm not sure how to change the default from JPEG; however, when saving the file it gives you the option to save as a variety of file types - and several of these are the bitmat options (various versions), TIFF, GIF, or PNG.  If you save this way (as bitmaps and not as a JPEG), you should be able to open them with Adobe (you should upgrade to Adobe Reader 9 at www.adobe.com) and nitro PDF as you were able to do before.

Good luck and I hope this helps!

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Lorien - One - MCSE/MCSA/Network+/A+