odd behavior indeed, can you tell which files are not being shown ?
on fat32 i think there is a limit in a folder of 65'535 files fat 16 is just 512 but its maximum size is 2gb so that isn't it.

Generally you can connect your camera to the computer by usb lead and it should identify itself as a mass storage device or additional drive.
It maybe possible to transfer files over that way.

It might be your card reader, particularly if its fairly old. Some of them can't handle large card sizes. I would expect a failure to read the card at all thou, so thats probably a long shot.

How are you handling your card? do you switch your camera off before removing or inserting the card? It is possible that you might be interrupting the card while it is writing that is usually bad news.

Of course it could be a flakey sd card but if the card is readable in the camera and if after the card has been in your PC the missing images show up on the camera well that seems unlikely too.

I think the best course of action would be to attach the camera via a usb cable to your computer and see if you can copy them that way.

Secondly I would see if the pictures transfer ok with a different card reader on a different PC if successful try that card reader on your PC.

Once you have recovered your images, i'd try filling the card with images on your pc (most of us have plenty of images). see if they are reliably stored.

If the card has been on 2 cameras you generally have a folder called dcim and two subfolders one storing one cameras images and one storing the other cameras images. Another thing is that say i had been shooting on monday and tuesday i would have a folder with mondays shots and another with tuesdays shots. On the camera i could browse them all as 1 long slide show but on the computer i would just see one days worth at a time. if i didn't know each day went into a different folder i might think that some were missing.

One other thing you might try is going to a photo lab locally one where they have little workstations where you can pick which images you want to print. Let the machine scan your card and see if it finds them all.
If it does you have isolated the problem to be with your PC and not the card.

so try usb transfer
try a different pc
try the supermarkets photo machine.

If still no success its worth talking to a pc repair guy, not a shop assistant. it will probably be um convenient if you have your sdcard with you. He may well take a look at it and tell you if he thinks its damaged.