Ok, I figured it out, but posted the thread anyone for reference for others as I spent far too much time looking through the boards for ANY info.
I had not used my Nook Color in awhile and after charging it, I immediately turned wi-fi off so I could see the status of the magazines that were missing on Nook for PC. They were there. Since I had uncovered the topic of losing magazines after 10 issues unless you archive them and then unarchive them, I archived all of my magazines. I then reconnected to wi-fi and unarchived the ones that I thought I may need in the next month. This meant I had to redownload them as well (which my system is currently doing.) To my relief, none of my magazines went awol.
Clicking back in Nook for PC (which I restarted twice, once due to machine pop-up and the other to make sure there wasn't a syncing issue), I noticed I still only had 1 copy of each magazine, but an odd thing with the current cover occasionally was duplicated in the archived side. I still had less than 40 mags by the applications count on the left toolbar.
When I clicked on a mag that I should have multiple issues, I now noticed I had the options for others when I clicked the "details" button. This gave a pop-up of other issues I could download, but I would not be able to see the COVER of the magazine until I opened it. Only the cover of the current one and then I can opt to select dates for other version (and guess if it is the one I want.) As a software designer, I find this to be horrible, but since it's only on my Nook for PC and NOT my Nook Color, I'm not going to worry about it.
Now I have to figure out why my Nook Color did NOT download 1.4. This is an ongoing problem for me whenever an update comes out, and is a bit of a pain to have to always sideload it. Was a bigger problem on my old nook color that crashed frequently and had to be reset. B&N really need to concern a "pull" update option for the nook color in case it does not do the automatic one that seems to be so elusive to some.
