I had a very similar problem for the past few weeks.. Galaxy Note N7100 with SanDisk ultra 32GB class 10.
Would show the same "Preparing SD Card" thing and then "Safe to remove." Would show up every single time I restarted the phone. Problem didn't show up until at least a month of using the phone/card. I now suspect that it was because a friend tossed the phone back to me on the bed while I was sleeping, phone bounced on the bed...which may have momentarily unseated the SD Card, thus removing it without un-mounting. After that the problem would happen every single time I restarted my phone.
Initially I got around it by first letting the phone do the scan, then restarting the phone when it showed safe to remove, and then locking the screen. It would be fine afterwards. But I eventually got frustrated as anyone would who spent so much money on getting the best equipment.
Also, the card did have folders that had been copied and renamed beginning with a "mju" character, and I eventually did start having problems even moving files from my internal memory to external.
Today I went through the forums, and did the following, which completely solved my problem (so far, so good!) and none of that "Preparing SD Card..." and "Safe to remove" rubbish shows up anymore when I start or restart my phone:
1. Backed up all my data by removing the card, and inserting directly into computer.
2. Reinserted and did a format on my phone. Format took like half a second, but I had my doubts about how little time it took the phone to wipe 22 gigs of data and format a card! (even though the "restart test" showed that it no more did the "Preparing SD Card" thing) but for good measure, I inserted the card back into my computer, did a FULL exFAT format with a 64 bit cluster size. Took almost an hour.
3. Reinserted into my phone to check. Things were somehow even faster now. And no more errors still.
4. Returned all my data to the card (took around 3 hours to return 22 gigs of data back to the newly formatted SD Card)
5. No problem whatsoever ever since.
6. For good measure, I have stuck a piece of scotch tape going over both sides of the SD Card to make it an even tighter fit inside the slot and protect against unseating the card if the phone is dropped or handled roughly. This Samsung model does seem to have an SD Card slot that doesn't feel quite as well made to me as my previous Nokia devices.
N.B: When I bought the card, I hadn't bothered with any formatting. Just slapped it into the device like I always do, but from now on, I will properly format a card as a matter of good practice before using, esp. when it's a 32G or above card.