suggestion to format the drive: i believe that would remove the information Windoze uses on load to recognize it; would remove the "system information" folder.
I should have qualified that suggestion with: "Backup your data first!!!
because it will be lost". Aside from that, there shouldn't be a 'system information' folder on the drive. I have a couple flash drives that I use to move data from win to nix to osx and neither have a 'system information' folder. Has your flash drive ever been loaded with a live version of winXP, or U3 software? If yes then I think you will definitely be wanting to scrub the drive clean. I've specifically read about the "pain" that can be caused from the U3 software, and the troubles to remove all of the remnants of the U3 app.
1) sometimes long time to read the card when opening the file system for it
I would hope that it's related to the mounting/umounting issue and that by fixing the issue would alleviate this problem, but you never know.
2) never recognized unless present at boot; not recognized if removed or inserted after boot, except to unmount it if removed when present at boot.
Back to basics on this one. Reboot your system without the flash drive attached. Once booted, insert the flash drive (the expectation is that it will not be automatically mounted). Then run lsusb - can you identify the device? If yes, can you then manually
mount the drive? If no, then (guru needed) is there a manual way to force a recheck of the USB hubs or all connected hardware (udev function??).