LR3 Syncronize folder finds "missing" photos that are not missing

Having switched to LR3 I made some new catalogs and syncrnized some folders.  LR3 kept find a ton of missing photos though and I was sure they were not missing.  SO I clicked on the "show missing files" button and sure enough it just showed me hundreds of photos that were not actually missing.  I checked them by right clicking on them and using the "show in finder" option to check that they were indeed still on my disk.
Whats happening ?  It seems to do it every time and I have tried it with several folders.  Every time it thought it found hundreds of missing photos.

Melissa,
I did not upgrade my catalog from LR2 to 3 , instead I started an entirely new catalog. I was hoping then to import some old LR2 catalogs into the new LR3 one but alas that plan has fallen foul of the import bug that effects importing catalogs with the same folders in them so I cant do that..... but thats all in another thread.
I think maybe I was not clear enough becuase it sounds like you didnt quite catch my point.  My point is that the photos are not missing at all, they ares still clrearly displayed in the catalog and I can double click them and open them no problem.  I do not have to locate them at all. They are still there.  It is just lightroom saying they are not there when i sync a folder.
So to clarify, when i syncronize,it tells me that X number of files are missing.  If I click the button to "show missing files"  all the photos that it shows, are still there.  It does not display them as missing, it displays them as normal.  Now this would not reall be a problem except that the sync default is to remove missing files.  So if you leave that option selected, LR removes a ton of files that were not missing!
Does that make it clearer, sorry i was not so clear the first time.

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