This is a known bug that has been in the firmware on the Touch for a while. The device doesn't load the SD card properly when restarted. It does see the card as it does something when you eject it. And when you connect to a PC, the PC can see the card.
The workaround, as you have found, is to eject the card and insert while the device is running. And if you change the sleep options to never power off, you will rarely see the problem.
Kobo do know about the problem, but haven't done anything to fix it.
For the collections problem, make sure the device has seen the books on the card and then connect to the PC and run calibre. If you have the options set to do collection management, it should create the collections. After that, they should appear on the device whenever it fully recognises the card.
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