Here's a surefire solution on how to solve the chrome icon problem. However, this procedure will take some time & effort.
Clear all browsing history incl. cache with chrome's History cleaner
Close chrome - Re-open
Click on each URL (revisit each webpage) in the Bookmark Manager followed by a page refresh (reload):
a) Bookmarks bar
b) Other Bookmarks
c) Imported Bookmarks (non IE bookmarks)
Under Bookmark Manager->Organize Export Bookmarks to HTML file into the folder of a newly created directory of your choice. Name the file folder therein 'Chrome bookmarks'
Do not close chrome before doing the next step!
Go to "C:\Users(User name)\AppData\Local\Google\Chrome\User Data\Default"
Copy the two files 'Favicons' and 'Favicons-journal' into the newly created file folder 'Chrome bookmarks'
For the time being make a note of the size of the 'Favicons' file you just saved
For testing purposes: before closing the chrome browser run chrome's History-> 'Clear browsing data'
Close browser - Reopen
Testresults: In all likelihood the 'Favicons' file located in "C:\Users(User name)\AppData\Local\Google\Chrome\User Data\Default" will show a file size much lower (~20-30k) than the one you saved into the exported file folder.
To resolve the missing icon problem: copy/paste the two saved 'Favicons' files from the new folder (see 4. above) to "C:\Users(User name)\AppData\Local\Google\Chrome\User Data\Default". Restart chrome. Your icons should be in place now nice and neatly. Just remember to check the file size of the default 'Favicons' file every once in awhile, especially after adding new bookmarked webpages. Then just copy the larger size default file to your 'Chrome bookmarks folder'. Voilà! This should work for most users.
For ease of recovering future lost icons add these two file locations to the Windows explorer's Favorites bar:
a) 'Chrome bookmarks'
b) "C:\Users(User name)\AppData\Local\Google\Chrome\User Data\Default"
PS in future use a browser history cleaner utility i.e. ccleaner. Avoid using chrome's History cleaning feature