Okay, I didn't find any I/O event items in red or otherwise.
I ran chkdsk F and then R for good measure. It fixed "errors in the uppercase file" and ended with:
488384000 KB total disk space.
369978700 KB in 207818 files.
108888 KB in 85175 indexes.
0 KB in bad sectors.
379216 KB in use by the system.
65536 KB occupied by the log file.
117917196 KB available on disk.
4096 bytes in each allocation unit.
122096000 total allocation units on disk.
29479299 allocation units available on disk.
I don't understand why I can see folders with books and calibre doesn't show that stuff. Can you explain as simply as possible how to fix this? I appreciate your help.