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Calibre will only import ebook types it knows about. Under Windows, this depends on the filename extension, i.e. it tries to import files with known extensions (e.g. .epub, .mobi, .lit, etcetera).
Open Calibre, and look in the category pane (I have this on the left). Click on the arrow by Formats and it will expand to show how many ebooks you have in each format. If you have not yet converted between formats, this should show exactly what was imported. If the list says there are 500 (say) EPUBs in your library, search the folders you imported for .epub (under Windows 7 this should be a file filter, type:=.epub). The bottom left of the search listing includes the number of items found. The number of items found should be about the same as the number that Calibre imported.
If they are very different, you may want to try again. Advise about mass import is hard to give because it depends on how you have organized your ebooks. What I tend to do is to use "Add books from a single directory". I also typically select one ebook type (e.g. EPUB) at a time and then left click on the 1st ebook to import and shift left click on the last (to select all listed between the two). I do this in small batches, because I want to edit the metadata after they get imported.
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