I cannot imagine why the My Clippings.txt file would have any effect. As far as the Kindle is concerned, it is just another TXT format ebook on your Kindle, with the proviso that the highlight/annotate/bookmark feature in the reader app will
log to that file,
for export purposes.
So I am pretty sure it must be the rebooting/charging.
I have no idea under what circumstances Amazon's code may develop memory leaks, you should probably ask them.
They have rejected all our requests for their proprietary source code...
...
FWIW, my Kindle Touch has never had these kinds of problems, except for slowness while manipulating collections while having (currently) ~1000 books.
Also, running some thirdparty aftermarket addons (i.e. "hacks") will occasionally crash things. (At least the alternative browser certainly does, it is after all a work-intensive piece of software...)