I had a quite similar problem after installing Kmon and KOReader. My problem was some thing like this: I connect my Glo HD to my computer then I transfer some epubs. Later, when I eject my Glo HD, it remains blocked during may be 20 mn or even more, but after if I reboot it (long pressing the power button on the top) it works, while still needing 20 mn to boot though.
I suspect that when installing KOReader, a lot of "small" files are added to the system and are parsed each time hence the slowness.
My solution was to completely remove Kmon and KOReader, and no more problems. I read some where though (I don't remember where) that when installing KOReader, one should inhibit the system to parse some directories (maybe the .adds) to prevent such behavior.
I don't know if it is the same problem as you have, but it seems at least to be the same symptoms.
Hopping you can fix it.
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